Help for package adegraphics

Type:

Package

Title:

An S4 Lattice-Based Package for the Representation of Multivariate Data

Version:

1.0-22

Description:

Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.

Depends:

R (≥ 3.0.2)

License:

GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

Imports:

ade4 (≥ 1.7-13), graphics, grid, KernSmooth, lattice, latticeExtra, methods, RColorBrewer, sp (≥ 1.1-1), stats

Suggests:

car, Guerry, knitr, markdown, pixmap, rmarkdown, spdep, splancs

Collate:

adeGsenv.R parameter.R utils.R utilstriangle.R genericMethod.R utilsclass.R panelfunctions.R ADEg.R ADEgS.R utilsADEgS.R ADEg.C1.R C1.barchart.R C1.curve.R C1.curves.R C1.density.R C1.gauss.R C1.dotplot.R C1.hist.R C1.interval.R ADEg.S1.R S1.boxplot.R S1.class.R S1.distri.R S1.label.R S1.match.R ADEg.S2.R S2.arrow.R S2.class.R S2.corcircle.R S2.density.R S2.distri.R S2.image.R S2.label.R S2.logo.R S2.match.R S2.traject.R S2.value.R ADEg.T.R T.image.R T.value.R T.cont.R ADEg.Tr.R Tr.class.R Tr.label.R Tr.match.R Tr.traject.R addhist.R addline.R addpoint.R addsegment.R addtext.R ade4-kplot.R ade4-scatter.R ade4-score.R ade4-plot.R multiplot.R s.Spatial.R utilskey.R

URL:

http://pbil.univ-lyon1.fr/ADE-4/

BugReports:

https://github.com/adeverse/adegraphics/issues

Encoding:

UTF-8

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2025-04-07 08:38:49 UTC; siberchicot

Author:

Stéphane Dray

[aut], Aurélie Siberchicot

[aut, cre], Jean Thioulouse

[ctb], Alice Julien-Laferrière [ctb]

Maintainer:

Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Repository:

CRAN

Date/Publication:

2025-04-07 09:10:02 UTC

Graphical objects for ade4 functions (and more)

Description

This package was created to replace graphics functionalities of the ade4 package and to offer customizable representations of data and result analysis.

Graphics are objects of S4 class, which can be displayed but also stored for latter modifications. Those modifications can be graphical changes, but also superposition or juxtaposition of various graphical objects (creating an other type of object). Each object will contain graphical parameters and instructions for the display (calls, positions, etc.) and the data set used. Sometimes data is heavy, due to its size for example. Two storing systems exist:

full storage: data is assigned to an object's slot.
names and position: data names (as a string, obtained using deparse(substitute)) and their frame position (using sys.nframe()) are stored. Then the full data can be retrieve with those two informations (and only if the data objects are still in the environment)

This new system is based on the lattice package and grid graphics.

Details

A lot of classes were implemented. Two superclass structures the architecture in class. Simple and complex graphics are distinguished in the former version:

ADEg class provides simple graphics using one kind of data (most of a time, only a data frame) and one representation method (points, labels, arrows...)
ADEgS class provides complex graphics making juxtaposition, superposition and/or insertion of several simple graphics.

5 subclasses inherits from the superclass abstract ADEg:

ADEg.S1: one-dimensional plot
ADEg.S2: bi-dimensional plot
ADEg.C1: one-dimensional data plotted in 2-D
ADEg.T: table plot
ADEg.Tr: triangle plot

References

Aurélie Siberchicot, Alice Julien-Laferrière, Anne-Béatrice Dufour, Jean Thioulouse and Stéphane Dray (2017). adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data. The R Journal. 9:2. 198–212. https://journal.r-project.org/archive/2017/RJ-2017-042/index.html

Examples

  showClass("ADEg")
  showClass("ADEgS")

Class `ADEg`

Description

An object of ADEg class is a simple graphic. This object can be blended in with another one (superposition, insertion and/or juxtaposition) to form a more complex graphics (an ADEgS object).

The ADEg class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class has five son classes : ADEg.S1, ADEg.S2, ADEg.C1, ADEg.T and ADEg.Tr.

Objects from the Class

None object of this class can be instantiated.

Slots

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

graphictype: the lattice function to use
arguments: its parameters to obtain the trellis object

g.args

a list containing some parameters linked with the created object of ADEg class:

xlim, ylim
main, sub
xlab, ylab
samelimits
scales: a list of scales informations (ticks, marks and labels for the x-axis or the y-axis) in the form of the lattice argument scales in the xyplot function

stats

a list of internal preliminary calculations

s.misc

a list of some other internal parameters

Call

an object of class call

Methods

panelbase: signature(object = "ADEg"): draws grid and text and produces graphical output from the graphical object
getcall: signature(object = "ADEg"): returns the Call slot
getlatticecall: signature(object = "ADEg"): returns the lattice.call slot
getstats: signature(object = "ADEg"): returns the stats slot
getparameters: signature(object = "ADEg", number): if number is 1, returns the trellis.par slot, if it is 2, returns the adeg.par slot and if it is 0, returns the both slots
add.ADEg: signature(object = "ADEg"): superposes an ADEg on the current one plotted
+: signature(e1 = "ADEg", e2 = "ADEg"): superposes e2 on e1
superpose: signature(g1 = "ADEgORtrellis", g2 = "ADEgORtrellis", which = "ANY", plot = "ANY"): creates a new ADEgS object performing a superposition of g2 on g1.
printSuperpose: signature(g1 = "ADEgORtrellis", refg = "ADEgORtrellis"): internal method, not for users.
cbindADEg: signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2.
rbindADEg: signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2 by rows.
insert: signature(graphics = "ADEgORtrellis", oldgraphics = "missing", posi, ratio, inset, plot, which): creates a new ADEgS object performing an insertion of graphics into the current device.
insert: signature(graphics = "ADEgORtrellis", oldgraphics = "ADEg", posi, ratio, inset, plot): creates a new ADEgS object performing an insertion of graphics into oldgraphics.
show: signature(x = "ADEg"): prints the ADEg object
plot: signature(x = "ADEg"): prints the ADEg object
print: signature(x = "ADEg"): displays the ADEg object in the current device or in a new one
update: signature(object = "ADEg"): modifies graphical parameters after the ADEg creation, updates the current display and returns the modified ADEg

Note

For any ADEg creation, various graphical parameters can be passed into the dots (...) arguments.

the parameters listed in adegpar() can be changed, even if some of them do no modify the graphic representation chosen.
the lattice parameters listed in trellis.par.get() can also be changed.
limits, main and sub title, and axes labels can be changed using the keys xlim, ylim, main, sub, xlab and ylab.
a neighbouring graph (object of class nb or listw) and a spatial one (object of class sp) can be display in the background using the keys nbobject, Sp and sp.layout.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("ADEg")

Class `ADEg.C1`

Description

An object of ADEg.C1 class represents unidimensional data into two dimensions.

The ADEg.C1 class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has three son classes : C1.barchart, C1.curve, C1.density, C1.dotplot, C1.gauss, C1.hist, C1.interval

Objects from the Class

None object of this class can be instantiated.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

graphictype: xyplot
arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

hori.update: a logical indicating if the sense of direction of the graphics is updating
backgrid: a list of two elements for grid lines. backgrid$x defines the coordinates of the lines (horizontal or vertical depending on the graphics orientation) and backgrid$d the grid mesh

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare: signature(object = "ADEg.C1"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
setlatticecall: signature(object = "ADEg.C1"): prepares the lattice.call slot
panelbase: signature(object = "ADEg.C1"): defines the graphical background (e.g. grid, rugs and box)
gettrellis: signature(object = "ADEg.C1"): converts the graphic into a trellis object of lattice class

Note

The ADEg.S1 class and ADEg.C1 class are both used to represent an unidimensional information (e.g. a score). The difference between these two classes is mainly ideological : an ADEg.S1 object is a representation into one dimension (e.g. one line) while an ADEg.C1 object is a representation into two dimensions (e.g. curves).

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("ADEg.C1")

Class `ADEg.S1`

Description

An object of ADEg.S1 class represents unidimensional data into one dimension.

The ADEg.S1 class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has five son classes : S1.boxplot, S1.class, S1.distri, S1.label and S1.match.

Objects from the Class

None object of this class can be instantiated.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

graphictype: xyplot
arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

hori.update: a logical indicating if the sense of direction of the graphics is updating
backgrid: a list of two elements for grid lines. backgrid$x defines the coordinates of the lines (horizontal or vertical depending on the graphics orientation) and backgrid$d the grid mesh
rug: an index value indicating where the rugs are drawn

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare: signature(object = "ADEg.S1"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
setlatticecall: signature(object = "ADEg.S1"): prepares the lattice.call slot
panelbase: signature(object = "ADEg.S1"): defines the graphical background (e.g. grid, rugs and box)
gettrellis: signature(object = "ADEg.S1"): converts the graphic into a trellis object of lattice class
zoom: signature(object = "ADEg.S1", zoom = "numeric", center = "missing"): performs a zoom in (if zoom < 1) or out (if zoom > 1) centered, only in one-dimension
zoom: signature(object = "ADEg.S1", zoom = "numeric", center = "numeric"): performs a zoom in (if zoom < 1) or out (if zoom > 1) around the center passed in parameter, only in one-dimension

Note

Various graphical parameters are used for display an ADEg.S1 object. The list p1d in adegpar() is thought specific for ADEg.S1 objects.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("ADEg.S1")
adegpar("p1d")

Class `ADEg.S2`

Description

An object of ADEg.S2 class represents bi-dimensional data.

The ADEg.S2 class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has eleven son classes : S2.arrow, S2.class, S2.corcircle, S2.density, S2.distri, S2.image, S2.label, S2.logo, S2.match, S2.traject and S2.value.

Objects from the Class

None object of this class can be instantiated.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

graphictype: xyplot
arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class:

fullcircle: only for S2.corcircle objects
method: only for S2.value objects
symbol: only for S2.value objects
center: only for S2.value objects

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

xfullcircle.update and yfullcircle.update: a logical indicating if the circle size is updating (only for S2.corcircle objects)
plegend.update: a logical indicating if the legend parameters are updating
breaks.update: a logical indicating if the legend breaks are updating
backgrid: a list of elements for grid lines

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare: signature(object = "ADEg.S2"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
setlatticecall: signature(object = "ADEg.S2"): prepares the lattice.call slot
panelbase: signature(object = "ADEg.S2"): defines the graphical background (e.g. grid and box)
gettrellis: signature(object = "ADEg.S2"): converts the graphic into a trellis object of lattice class
zoom: signature(object = "ADEg.S2", zoom = "numeric", center = "missing"): performs a zoom in (if zoom < 1) or out (if zoom > 1) centered
zoom: signature(object = "ADEg.S2", zoom = "numeric", center = "numeric"): performs a zoom in (if zoom < 1) or out (if zoom > 1) around the center passed in parameter (center should be a two-length vector)
addhist: signature(object = "ADEg.S2"): adds histograms and density lines against a bi-dimensional graphics

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("ADEg.S2")

Class `ADEg.T`

Description

An object of ADEg.T class represents table data.

The ADEg.T class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has two son classes : T.image and T.value.

Objects from the Class

None object of this class can be instantiated.

Slots

data:

a list containing data or data's name.

dftab: the displayed values which can be table, dist or matrix in the form of a data frame, a name or a matching call
coordsx: an integer or a vector indicating the columns of dftab kept
coordsy: an integer or a vector indicating the rows of dftab kept
labelsx: the columns' labels
labelsy: the rows' labels
"frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

graphictype: xyplot
arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.T class:

method: only for T.value objects
symbol: only for T.value objects
center: only for T.value objects

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

breaks.update: a logical indicating if the legend breaks is updating
axes$dx and axes$dy: intervals for the cell size

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare: signature(object = "ADEg.T"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
setlatticecall: signature(object = "ADEg.T"): prepares the lattice.call slot
panelbase: signature(object = "ADEg.T"): defines the graphical background (e.g. axes, labels, ticks, box and grid)
gettrellis: signature(object = "ADEg.T"): converts the graphic into a trellis object of lattice class

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("ADEg.T")

Class `"ADEg.Tr"`

Description

An object of ADEg.Tr class represents triangular coordinates in 2D.

The ADEg.Tr class is a virtual class, i.e. a class which is not possible to create objects but which have heirs. This class inherits from ADEg class and has three son classes : Tr.class, Tr.label, T.match and T.traject.

Objects from the Class

None object of this class can be instantiated.

Slots

data:

a list containing data or data's name.

dfxyz: the displayed values in the form of a data frame with three columns, a name or a matching call.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list of two elements to create the trellis object:

graphictype: xyplot
arguments: its parameters to obtain the trellis object

g.args

a list containing some method parameters linked with the created object of ADEg.Tr class:

max3d and min3d: triangular limits
adjust: a logical to adjust the device with the limits

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

adjust.update: a logical indicating if the adjust slot is updating
cornerp: coordinates of the triangle extremities.
lgrid: a list containing the three coordinates of the grid segments extremities(pts1, pts2, pts3) and the value of the division (posgrid)

Call

an object of class call

Extends

Class ADEg, directly.

Methods

prepare: signature(object = "ADEg.Tr"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
setlatticecall: signature(object = "ADEg.Tr"): prepares the lattice.call slot
panelbase: signature(object = "ADEg.Tr"): defines the graphical background (e.g. triangle and grid)
gettrellis: signature(object = "ADEg.Tr"): converts the graphic into a trellis object of lattice class

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("ADEg.Tr")

Creation of `ADEgS` objects

Description

Creates and displays an "ADEgS" object, a set of ADEg, trellis and/or ADEgS objects, managed by superposition, insertion and/or juxtaposition.

Usage

ADEgS(adeglist, positions, layout, add = NULL, plot = TRUE)

Arguments

adeglist

a list of several trellis, ADEg and/or ADEgS objects.

positions

a matrix with four columns and as many rows as the number of graphical objects in ADEglist slot. For each simple graphic, i.e. in each row, the coordinates of the top-right and the bottom-left hand corners are in npc unit (normalized parent coordinates).

layout

a layout indication in two possible forms:

a list containing arguments of the layout function
a two-length vector containing rows' and columns' number of layout

add

a square matrix with as many rows and columns as the number of graphical objects in the ADEglist slot. The value at the i-th row and j-th column is equal to 1 whether the j-th graphical object in ADEglist slot is superpose to i-th graphical one. Otherwise, this value is equal to 0.

plot

a logical. If the graphics should be displayed

Value

an ADEgS object. If plot = TRUE, the created object is displayed.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

xy <- matrix(rnorm(20), ncol = 2)
g1 <- s.label(xy)
g2 <- s.class(xy, fac = as.factor(rep(LETTERS[1:2], length.out = 10)), ppoints.cex = 0,
  col = c("blue", "red"))
g3 <- ADEgS(list(g1, g2), rbind(c(0, 0, 0.5, 1), c(0.5, 0, 1, 1)))
g4 <- ADEgS(list(g1, g2), layout = c(2, 1))
g5 <- ADEgS(list(g1, g2))
g6 <- ADEgS(list(g1, g2), add = matrix(c(0, 1, 0, 0), byrow = TRUE, ncol = 2))

data(olympic, package = "ade4")
dudi1 <- ade4::dudi.pca(olympic$tab, scan = FALSE)
g7 <- s.arrow(dudi1$li)
g8 <- s.corcircle(dudi1$co, lab = names(olympic$tab))
g9 <- ADEgS(list(g7, g8), rbind(c(0, 0, 0.5, 1), c(0.5, 0, 1, 1)))
g9[[1]]
g9[1, drop = FALSE]
length(g9)

Class `"ADEgS"`

Description

An object of ADEgS class is a complex graphic. This class allows the superposition, the insertion and/or the juxtaposition of several ADEg, trellis and/or ADEgS objects.

The ADEgS class have neither father class nor son classes.

Objects from the Class

ADEgS objects can be created by calls of the form new("ADEgS", ...).

The regular usage in this package is to use the ADEgS, add.ADEg, superpose, insert or + functions.

Slots

ADEglist: a list of several trellis, ADEg and/or ADEgS objects.
positions: a matrix with four columns and as many rows as the number of graphical objects in the ADEglist slot. For each simple graphic, i.e. in each row, the coordinates of the top-right and the bottom-left hand corners are in npc unit (normalized parent coordinates).
add: a square matrix with as many rows and columns as the number of graphical objects in the ADEglist slot. The value at the i-th row and j-th column is equal to 1 whether the j-th graphical object in the ADEglist slot is superpose to i-th graphical one. Otherwise, this value is equal to 0.
Call: an object of class call

Methods

[: signature(x = "ADEgS", i = "numeric", j = "missing", drop = "logical"): extracts the i-th sub-graphics in the x@ADEglist. i can be a vector. If i is a single number and if the extracted graphic in an ADEg object, the sub-selection is in the form of ADEg if drop is TRUE and in the form of ADEgS otherwise.
[: signature(x = "ADEgS", i = "numeric", j = "missing", drop = "missing"): the same than the previous method. drop is FALSE by default
[[: signature(x = "ADEgS", i = "numeric", j = "missing"): extracts one sub-graphic, the i-th one, in the x@ADEglist
[[: signature(x = "ADEgS", i = "character", j = "missing"): extracts one sub-graphic, named i in the x@ADEglist
[[<-: signature(x = "ADEgS", i = "numeric", j = "missing", value = "ADEg"): replaces one sub graphic, the i-th one, by an ADEg object in the x@ADEglist
[[<-: signature(x = "ADEgS", i = "numeric", j = "missing", value = "ADEgS"): replaces one sub graphic, the i-th one, by an ADEgS object in the x@ADEglist
$: signature(x = "ADEgS"): extracts one sub-graphic by its name in the x@ADEglist
getpositions: signature(object = "ADEgS"): returns the positions matrix of the object, i.e. object@positions
getgraphics: signature(object = "ADEgS"): returns the list of graphics of the object, i.e. object@ADEglist
getcall: signature(object = "ADEgS"): returns the call of the object, i.e. object@Call
names: signature(object = "ADEgS"): returns the graphics' names of the object, i.e. the names of object@ADEglist
names<-: signature(object = "ADEgS"): replaces the graphics' names of the object, i.e. the names of object@ADEglist
length: signature(x = "ADEgS"): returns the number of graphics into x, i.e. the length of x@ADEglist
plot: signature(x = "ADEgS"): same as print
print: signature(x = "ADEgS"): displays the graphical elements into one device using positions and superposition management (x@add matrix)
show: signature(object = "ADEgS"): same as print
superpose: signature(g1 = "ADEgS", g2 = "ADEg", which = "numeric", plot = "logical"): creates a new "ADEgS" object performing a superposition of g2 on the which-th ADEg object of g1. This object is printed if plot is TRUE.
superpose: signature(g1 = "ADEgS", g2 = "ADEg", which = "numeric", plot = "ANY"): creates a new "ADEgS" object performing a superposition of g2 on the which-th ADEg object of g1. This object is printed only if plot is TRUE.
superpose: signature(g1 = "ADEgS", g2 = "ADEg", which = "missing", plot = "ANY"): creates a new "ADEgS" object performing a superposition of g2 on the last ADEg object of g1. This object is printed only if plot is TRUE.
superpose: signature(g1 = "ADEgS", g2 = "ADEgS", which = "missing", plot = "ANY"): creates a new "ADEgS" object performing a superposition between two ADEgS having the same length and the same positions slot. It is used when g1 and g2 are both created with a partition of individual groups, variables or analysis' axis.
+: signature(e1 = "ADEg", e2 = "ADEgS"): creates a new "ADEgS" object performing a superposition of e1 on e2.
+: signature(e1 = "ADEgS", e2 = "ADEg"): creates a new "ADEgS" object performing a superposition of e2 on e1.
cbindADEg: signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2 by columns.
rbindADEg: signature(g1 = "ADEgORADEgS", g2 = "ADEgORADEgS"): creates a new "ADEgS" object combining g1 on g2 by rows.
update: signature(object = "ADEgS"): modifies the graphical parameters of each sub-graphics listed in object@ADEglist and/or the object's names (with the key word names) and/or the object@positions slot (with the key word positions), after creation of the object. The current display is updated and a modified object is returned.
insert: signature(graphics = "ADEgS", oldgraphics = "missing", posi, ratio, inset, plot, which, dispatch): creates a new "ADEgS" object performing an insertion of graphics into the current device.
insert: signature(graphics = "ADEgS", oldgraphics = "ADEg", posi, ratio, inset, plot): creates a new "ADEgS" object performing an insertion of graphics into oldgraphics.
insert: signature(graphics = "ADEgORtrellis", oldgraphics = "ADEgS", posi, ratio, inset, plot, which): creates a new "ADEgS" object performing an insertion of graphics into oldgraphics.
insert: signature(graphics = "ADEgS", oldgraphics = "ADEgS", posi, ratio, inset, plot, which, dispatch): creates a new "ADEgS" object performing an insertion of graphics into oldgraphics.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

  showClass("ADEgS")

Class `C1.barchart`

Description

A class for the creation and display of a numeric score using barcharts.

Objects from the Class

C1.barchart objects can be created by calls of the form new("C1.barchart", ...).

The regular usage in this package is to use the s1d.barchart function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a vector, a factor, a name or a matching call.
labels: the labels' names drawn on the top of bars.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slot for C1.barchart objects is:

sort: a logical indicating if score is sorted in ascending order.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.barchart are:

prepare: signature(object = "C1.barchart"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.
panel: signature(object = "C1.barchart"): draws bar charts and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.barchart")

Class `C1.curve`

Description

A class for the creation and display of a numeric score linked by curves. The C1.curves allows to deal with multiple scores.

Objects from the Class

C1.curve objects can be created by calls of the form new("C1.curve", ...). The regular usage in this package is to use the s1d.curve function.

C1.curves objects can be created by calls of the form new("C1.curves", ...). The regular usage in this package is to use the s1d.curves function. Class C1.curves extends C1.curve directly.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a vector, a factor, a name or a matching call.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.curve and C1.curves are:

prepare: signature(object = "C1.curve"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.
panel: signature(object = "C1.curve"): draws points and curves.
panel: signature(object = "C1.curves"): draws points and curves.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.curve")
showClass("C1.curves")

Class `C1.density`

Description

A class for the creation and display of a numeric score using density curves.

Objects from the Class

C1.density objects can be created by calls of the form new("C1.density", ...).

The regular usage in this package is to use the s1d.density function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
fac: a factor for score to split in the form of a vector, a factor, a name or a matching call.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slots for C1.density objects are:

kernel, bandwidth and gridsize: passed in parameters in bkde function of the KernSmooth package.
fill: a logical to yield the polygons density curves filled.
col: a logical, a color or a colors vector to color labels, rugs, lines and polygons.

stats

a list of internal preliminary calculations. The specific slot for C1.density objects is:

densit: the values of density curve calculated for each factor in fac computes with the bkde function of the KernSmooth package.

s.misc

a list of some others internal parameters. The specific slot for C1.density objects is:

rug: an index value indicating where the rugs are drawn

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.density are:

prepare: signature(object = "C1.density"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the density curves according to the numeric score and the values' categories.
panel: signature(object = "C1.density"): draws density curves.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.density")

Class `C1.dotplot`

Description

A class for the creation and display of a numeric score using dots.

Objects from the Class

C1.dotplot objects can be created by calls of the form new("C1.dotplot", ...).

The regular usage in this package is to use the s1d.dotplot function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a vector, a factor, a name or a matching call.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.dotplot are:

prepare: signature(object = "C1.dotplot"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.
panel: signature(object = "C1.dotplot"): draws segments and dots.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.dotplot")

Class `C1.gauss`

Description

A class for the creation and display of a numeric score using gauss' curves.

Objects from the Class

C1.gauss objects can be created by calls of the form new("C1.gauss", ...).

The regular usage in this package is to use the s1d.gauss function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
fac: a factor for score splitting in the form of a vector, a factor, a name or a matching call.
wt: a vector of weights for score
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slots for C1.gauss objects are:

fill: a logical to yield the gauss curves transparent.
col: a logical, a color or a colors vector to color labels, rugs, lines and polygons.
steps: a value for the number of segments used to draw Gauss curves.

stats

a list of internal preliminary calculations. The specific slots for C1.gauss objects are:

means: the weighted mean calculated for each fac value.
var: the weighted variance calculated for each fac value.
gausscurves: the density gauss curve calculated for each fac value.

s.misc

a list of some others internal parameters. The specific slot for C1.gauss objects is:

rug: an index value indicating where the rugs are drawn

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.gauss are:

prepare: signature(object = "C1.gauss"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the Gauss curves according to the numeric score and the values' categories (using weighted mean and standard deviation).
panel: signature(object = "C1.gauss"): draws Gauss curves and level names of each curve.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.gauss")

Class `C1.hist`

Description

A class for the creation and display of a numeric score using a histogram.

Objects from the Class

C1.hist objects can be created by calls of the form new("C1.hist", ...).

The regular usage in this package is to use the s1d.hist function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a vector, a factor, a name or a matching call.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slots for C1.hist objects are:

breaks: a vector of values to split score. If NULL, pretty(score, nclass) is used.
nclass: an integer for the number of desired intervals, ignored if breaks is not missing.
type: a value among count, density, percent to indicate the unit of the cell height.
right: a logical indicating if the histogram cells are right-closed (left open) intervals.

stats

a list of internal preliminary calculations. The specific slots for C1.hist objects are:

heights: the cell height.
breaks: the cell boundaries.

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.hist are:

prepare: signature(object = "C1.hist"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the boundaries and the height of cells.
panel: signature(object = "C1.hist"): draws rectangles.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.hist")

Class `C1.interval`

Description

A class for the creation and display of an interval between two numeric scores.

Objects from the Class

C1.interval objects can be created by calls of the form new("C1.interval", ...).

The regular usage in this package is to use the s1d.interval function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a vector, a factor, a name or a matching call.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.C1 class. The specific slot for C1.density objects is:

method: a value, bars or area, to represent either segments or areas between scores.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.C1, directly.
Class ADEg, by class ADEg.C1, distance 2.
Class ADEgORtrellis, by class ADEg.C1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.C1, distance 3.

Methods

The methods of the father classes "ADEg.C1" and "ADEg" can be used by inheritance. The specific methods for C1.interval are:

prepare: signature(object = "C1.interval"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default.
panel: signature(object = "C1.interval"): draws segments or polygons.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("C1.interval")

Class `S1.boxplot`

Description

A class for the representation of the link between a variable and a qualitative variable using box-and-whisker plots.

Objects from the Class

S1.boxplot objects can be created by calls of the form new("S1.boxplot", ...).

The regular usage in this package is to use the s1d.boxplot function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
fac: a factor for score splitting in the form of a vector, a factor, a name or a matching call.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class. The specific slot for S1.boxplot objects is:

col: a NULL value, a color or a colors vector to color points, labels, lines and polygons.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S1, directly.
Class ADEg, by class ADEg.S1, distance 2.
Class ADEgORtrellis, by class ADEg.S1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S1, distance 3.

Methods

The methods of the father classes "ADEg.S1" and "ADEg" can be used by inheritance. The specific methods for S1.boxplot are:

prepare: signature(object = "S1.boxplot"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default.
panel: signature(object = "S1.boxplot"): draws box-and-wiskers diagrams, mean points and labels.
setlatticecall: signature(object = "S1.boxplot"): prepares the lattice.call slot

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S1.boxplot")

Class `S1.class`

Description

A class for the creation and display of a numeric score aggregated in class by an associated factor.

Objects from the Class

S1.class objects can be created by calls of the form new("S1.class", ...).

The regular usage in this package is to use the s1d.class function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
fac: a factor for score splitting in the form of a vector, a factor, a name or a matching call.
wt: a vector of weights for score
labels: the labels' names drawn for each class.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class. The specific slots for S1.class objects are:

col: a NULL value, a color or a colors vector to color points, labels and lines.
poslabel: the label position of each class, it can be regular or value.

stats

a list of internal preliminary calculations. The specific slot for S1.class objects is:

means: the weighted mean calculated for each fac value.

s.misc

a list of some others internal parameters. The specific slot for S1.class objects is:

rug: an index value indicating where the rugs are drawn.

Call

an object of class call

Extends

Class ADEg.S1, directly.
Class ADEg, by class ADEg.S1, distance 2.
Class ADEgORtrellis, by class ADEg.S1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S1, distance 3.

Methods

The methods of the father classes "ADEg.S1" and "ADEg" can be used by inheritance. The specific methods for S1.class are:

prepare: signature(object = "S1.class"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default.
panel: signature(object = "S1.class"): draws labels and lines matching with score values.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S1.class")

Class `S1.distri`

Description

A class for the representation of a set of distributions on a numeric score.

Objects from the Class

S1.distri objects can be created by calls of the form new("S1.distri", ...).

The regular usage in this package is to use the s1d.distri function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
dfdistri: the mass distribution in which each column is a class.
labels: the labels' names drawn for each distribution.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class. The specific slots for S1.distri objects are:

sdSize: the size of the standard deviation segments.
yrank: a logical to draw the distributions sorted by means ascending order.

stats

a list of internal preliminary calculations. The specific slots for S1.distri objects are:

means: the weighted mean calculated for each distribution.
sds: the weighted variance calculated for each distribution.

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S1, directly.
Class ADEg, by class ADEg.S1, distance 2.
Class ADEgORtrellis, by class ADEg.S1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S1, distance 3.

Methods

The methods of the father classes "ADEg.S1" and "ADEg" can be used by inheritance. The specific methods for S1.distri are:

prepare: signature(object = "S1.distri"): calls the parent method (prepare for ADEg.S1), modifies some graphical parameters used by default and calculates weighted mean and standard deviation.
panel: signature(object = "S1.distri"): draws mean points and segments with matching labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S1.distri")

Class `S1.label`

Description

A class for the creation and display of a numeric score with labels.

Objects from the Class

S1.label objects can be created by calls of the form new("S1.label", ...).

The regular usage in this package is to use the s1d.label function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
labels: the labels' names drawn for each score value.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class. The specific slot for S1.class objects is:

poslabel: the label position of each score value, it can be "regular" or "value".

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters. The specific slot for S1.label objects is:

rug: an index value indicating where the rugs are drawn.

Call

an object of class call

Extends

Class ADEg.S1, directly.
Class ADEg, by class ADEg.S1, distance 2.
Class ADEgORtrellis, by class ADEg.S1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S1, distance 3.

Methods

The methods of the father classes "ADEg.S1" and "ADEg" can be used by inheritance. The specific methods for S1.label are:

prepare: signature(object = "S1.label"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default.
panel: signature(object = "S1.label"): draws labels and its links with score points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S1.label")

Class `S1.match`

Description

A class for the creation and display of paired scores.

Objects from the Class

S1.match objects can be created by calls of the form new("S1.match", ...).

The regular usage in this package is to use the s1d.match function.

Slots

data

a list containing data or data's name.

score: the displayed values in the form of a numeric vector, a name or a matching call.
labels: the labels' names drawn for each score.
at: the index value.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S1 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters. The specific slot for S1.match objects is:

rug: an index value indicating where the rugs are drawn.

Call

an object of class call

Extends

Class ADEg.S1, directly.
Class ADEg, by class ADEg.S1, distance 2.
Class ADEgORtrellis, by class ADEg.S1, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S1, distance 3.

Methods

The methods of the father classes "ADEg.S1" and "ADEg" can be used by inheritance. The specific methods for S1.match are:

prepare: signature(object = "S1.match"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default.
panel: signature(object = "S1.match"): draws score points and matching segments and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S1.match")

Class `S2.arrow`

Description

A class for creating and drawing bi-dimensional plot with arrows from the origin to the coordinates and labeled.

Objects from the Class

S2.arrow objects can be created by calls of the form new("S2.arrow", ...).

The regular usage in this package is to use the s.arrow function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
labels: a vector containing the arrows' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slot for S2.arrow objects is:

Sp: a spatial object stem from Sp package.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

lim.update: a logical indicating if the limits are updating

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.arrow are:

prepare: signature(object = "S2.arrow"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates limits.
panel: signature(object = "S2.arrow"): draws points, arrows and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.arrow")

Class `S2.class`

Description

A class for group representation in bi-dimensional plot.

Objects from the Class

S2.class objects can be created by calls of the form new("S2.class", ...).

The regular usage in this package is to use the s.class function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
fac: a factor (or a matrix of factors) splitting the rows of dfxy.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
wt: a vector of weights for fac.
labels: a vector containing the class' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slots for S2.class objects are:

ellipseSize: a positive number for ellipse size.
starSize: a number between 0 and 1 for star size.
chullSize: NULL or a vector of numbers between 0 and 1 for the convex hulls.
col: a logical or a vector of colors that apply to points, ellipses, labels, lines and polygons.

stats

a list of internal preliminary calculations. The specific slots for S2.class objects are:

means: a matrix containing the weighted mean calculated for each fac value.
covvar: a list containing the weighted variance-covariance matrices calculated for each fac value.

s.misc

a list of some others internal parameters:

ellipses: ellipses' coordinates.
chullcoord: convex hulls' coordinates.

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.class are:

prepare: signature(object = "S2.class"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates ellipses, convex hulls and centroids.
panel: signature(object = "S2.class"): draws ellipses, convex hulls, stars, labels and points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.class")

Class `S2.corcircle`

Description

A class for creating and drawing a correlation circle.

Objects from the Class

S2.corcircle objects can be created by calls of the form new("S2.corcircle", ...).

The regular usage in this package is to use the s.corcircle function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
labels: a vector containing the points' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slot for S2.corcircle objects is:

fullcircle: a logical to include the complete circle (limits are then c(-1, 1)).

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

backgrid: a list of elements for grid lines

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.corcircle are:

prepare: signature(object = "S2.corcircle"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and prepares the drawn grid.
panel: signature(object = "S2.corcircle"): draws arrows, labels and axes.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.corcircle")

Class `S2.density`

Description

A class for the creation and display of bi-dimensional plot with density estimation.

Objects from the Class

S2.density objects can be created by calls of the form new("S2.density", ...).

The regular usage in this package is to use the s.density function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slots for S2.density objects are:

bandwidth: bandwidth for density calculations which is passed in parameters in the bkde2D function of the KernSmooth package.
gridsize: grid dimension.
threshold: a value between 0 and 1 to draw densities greater than this threshold. No density is visible whether it is equal to 1.
col: a NULL value, a color or a colors vector to color densities.
nrpoints: number of points on the density image.
contour: a logical to draw contour lines.
region: a logical to fill grid regions with col.
nclass: number of class for density.

stats

a list of internal preliminary calculations. The specific slot for S2.density objects is:

densit: a list containing the results of the bkde2D function.

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.density are:

prepare: signature(object = "S2.density"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates densities.
panel: signature(object = "S2.density"): draws densities and external points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.density")

Class `S2.distri`

Description

A class for distributions on a numeric score using a mean-standard deviation display.

Objects from the Class

S2.distri objects can be created by calls of the form new("S2.distri", ...).

The regular usage in this package is to use the s.distri function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
dfdistri: the mass distribution in which each column is a class.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slots for S2.distri objects are:

ellipseSize: NULL or number between 0 and 1 for ellipse size.
starSize: NULL or number between 0 and 1 for star size.
col: a NULL value, a color or a colors vector to color ellipses, labels, lines and polygons.

stats

a list of internal preliminary calculations. The specific slots for S2.distri objects are:

means: a matrix containing the weighted mean calculated for each class indfdistri.
covvar: a list containing the weighted variance-covariance matrices calculated for each class indfdistri.

s.misc

a list of some others internal parameters:

ellipses: ellipses' coordinates.

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.distri are:

prepare: signature(object = "S2.distri"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates ellipses and centroids.
panel: signature(object = "S2.distri"): draws ellipses, stars, labels and points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.distri")

Class `S2.image`

Description

A class for the creation of a bi-dimensional plot with a third value represented as a continuous colored surface.

Objects from the Class

S2.image objects can be created by calls of the form new("S2.image", ...).

The regular usage in this package is to use the s.image function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
z: a vector (or a matrix) of values on the dfxy rows.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slots for S2.image objects are:

gridsize: a 1 or 2-length vector indicating the cell numbers (horizontally and vertically) of the grid for the colored surface.
outsideLimits: specific limits for the surface as a set of polygons. It must be an SpatialPolygons object. Hole are authorized.
span: a value to control the degree of smoothing.
contour: a logical to draw contour lines.
region: a logical to fill inter-contour regions.
col: a NULL value, a color or a colors vector used for the colored cells.

stats

a list of internal preliminary calculations. The specific slot for S2.image objects is:

value: a prediction value yielded by a local polynomial regression fitting.

s.misc

a list of some others internal parameters:

newgrid: the grid expansion calculated within the prepare method.

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.image are:

prepare: signature(object = "S2.image"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates grid expansion and limits.
panel: signature(object = "S2.image"): draws raster image.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.image")

Class `S2.label`

Description

A class for creating and drawing bi-dimensional plot with point label.

Objects from the Class

S2.label objects can be created by calls of the form new("S2.label", ...).

The regular usage in this package is to use the s.label function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
labels: a vector of character strings for the points' labels
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.label are:

prepare: signature(object = "S2.label"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default.
panel: signature(object = "S2.label"): draws points and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.label")

Class `S2.logo`

Description

A class for the creation of a bi-dimensional plot with pictures for points representation.

Objects from the Class

S2.logo objects can be created by calls of the form new("S2.logo", ...).

The regular usage in this package is to use the s.logo function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
logos: a list containing the picture to use for each point.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slot for S2.logo objects is:

rect: a logical to frame logos.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.class are:

prepare: signature(object = "S2.class"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default.
panel: signature(object = "S2.class"): displays the logos.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.logo")

Class `S2.match`

Description

A class for the creation and display of paired coordinates in a bi-dimensional plot.

Objects from the Class

S2.match objects can be created by calls of the form new("S2.match", ...).

The regular usage in this package is to use the s.match function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
labels: a vector of character strings containing the matches' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slot for S2.match objects is:

arrows: a logical to draw arrows.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.match are:

prepare: signature(object = "S2.match"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default.
panel: signature(object = "S2.match"): draws arrows and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.match")

Class `S2.traject`

Description

A class for the creation of a bi-dimensional plot with trajectories linking the points.

Objects from the Class

S2.traject objects can be created by calls of the form new("S2.traject", ...).

The regular usage in this package is to use the s.traject function.

Slots

data

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
fac: a factor (or a matrix of factors) splitting the rows of dfxy.
labels: a vector of character strings containing the trajectories' labels.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slots for S2.traject objects are:

order: a vector containing the drawing order of the trajectories. A vector of length equal to factor.
col: a NULL value, a color or a colors vector to color points, labels and lines.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.traject are:

prepare: signature(object = "S2.traject"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default.
panel: signature(object = "S2.traject"): draws points, arrows and labels.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("S2.traject")

Class `S2.value`

Description

A class for the creation and display of bi-dimensional plot with a third value represented (as a variable) by symbols.

Objects from the Class

S2.value objects can be created by calls of the form new("S2.value", ...).

The regular usage in this package is to use the s.value function.

Slots

data:

a list containing data or data's name.

dfxy: the displayed values in the form of a data frame, a name or a matching call.
z: a vector (or a matrix) with as many values as rows in dfxy.
xax: an integer or a vector indicating the columns of dfxy kept for the x-axes.
yax: an integer or a vector indicating the columns of dfxy kept for the y-axes.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.S2 class. The specific slots for S2.value objects are:

method: the method of representation for z (color shading or proportional size).
symbol: the type of symbol (square or circle).
center: a center value for method size.
centerpar: a logical or a list to represent center value using elements in the adegpar("ppoints") list.
breaks: a vector containing the breaks used for splitting z value. If NULL, pretty(z, n) is used.
nclass: an integer for the number of desired intervals, ignored if breaks is not missing.
col: a NULL value, a color or a colors vector to color symbols.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

plegend.update: a logical indicating if the legend parameters are updating
breaks.update: a logical indicating if the legend breaks are updating
lim.update: a logical indicating if the limits are updating

Call

an object of class call

Extends

Class ADEg.S2, directly.
Class ADEg, by class ADEg.S2, distance 2.
Class ADEgORtrellis, by class ADEg.S2, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.S2, distance 3.

Methods

The methods of the father classes "ADEg.S2" and "ADEg" can be used by inheritance. The specific methods for S2.value are:

prepare: signature(object = "S2.value"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates limits.
panel: signature(object = "S2.value"): draws symbols.

Note

For the symbol size, if the method is size, we use perceptual scaling (Tanimura et al. 2006).

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Tanimura, S. and Kuroiwa, C. and Mizota, T. 2006. Proportional symbol mapping in R. Journal of Statistical Software. 15, 1–7

Examples

showClass("S2.value")

Class `T.cont`

Description

A class for the representation of a contingency table object with statistical information (mean and regression lines).

Objects from the Class

T.cont objects can be created by calls of the form new("T.cont", ...).

The regular usage in this package is to use the table.value function with a table object.

Slots

data:

a list containing data or data's name.

dftab: a contingency table object in the form of a data frame, a name or a matching call
coordsx: an integer or a vector indicating the columns of dftab kept
coordsy: an integer or a vector indicating the rows of dftab kept
labelsx: the columns' labels
labelsy: the rows' labels
"frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of T.value class. The specific slots for T.cont objects are:

meanX: a logical to represent columns' means by points.
meanY: a logical to represent rows' means by points.
ablineX: a logical to represent columns' regression lines.
ablineY: a logical to represent columns' regression lines.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class T.value, directly.
Class ADEg.T, by class T.value, distance 2.
Class ADEg, by class T.value, distance 3.
Class ADEgORtrellis, by class T.value, distance 4.
Class ADEgORADEgSORtrellis, by class T.value, distance 4.

Methods

The methods of the father classes "T.value", "ADEg.T" and "ADEg" can be used by inheritance. The specific methods for T.cont are:

panel: signature(object = "T.cont"): draws mean points and regression lines.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("T.cont")

Class `T.image`

Description

A class for the representation of a matrix or table object in which values have different colors.

Objects from the Class

T.image objects can be created by calls of the form new("T.image", ...).

The regular usage in this package is to use the table.image function.

Slots

data

a list containing data or data's name.

dftab: the displayed values which can be table, dist or matrix in the form of a data frame, a name or a matching call
coordsx: an integer or a vector indicating the columns of dftab kept
coordsy: an integer or a vector indicating the rows of dftab kept
labelsx: columns labels
labelsy: rows labels
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.T class. The specific slots for T.image objects are:

breaks: a vector of values to split dftab. If NULL, pretty(dftab, nclass) is used.
nclass: an integer for the number of desired intervals, ignored if breaks is not missing.
col: a NULL value, a color or a colors vector used for the cells.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

breaks.update: a logical indicating if the legend breaks is updating.

Call

an object of class call

Extends

Class ADEg.T, directly.
Class ADEg, by class ADEg.T, distance 2.
Class ADEgORtrellis, by class ADEg.T, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.T, distance 3.

Methods

The methods of the father classes "ADEg.T" and "ADEg" can be used by inheritance. The specific methods for T.image are:

prepare: signature(object = "T.image"): calls the parent method (prepare for ADEg.T) and modifies some graphical parameters used by default and calculates limits and grid.
panel: signature(object = "T.image"): draws raster image.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("T.image")

Class `T.value`

Description

A class for the representation of a matrix, a data frame, or a distance matrix using symbols, varying in size or color.

Objects from the Class

T.value objects can be created by calls of the form new("T.value", ...).

The regular usage in this package is to use the table.value function.

Slots

data:

a list containing data or data's name.

dftab: the displayed values which can be table, dist or matrix in the form of a data frame, a name or a matching call
coordsx: an integer or a vector indicating the columns of dftab kept
coordsy: an integer or a vector indicating the rows of dftab kept
labelsx: the columns' labels
labelsy: the rows' labels
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.T class. The specific slots for T.value objects are:

breaks: a vector of values to split dftab. If NULL, pretty(dftab, nclass) is used.
nclass: an integer for the number of desired intervals, ignored if breaks is not missing.
col: a NULL value, a color or a colors vector to color symbols.
method: the method of representation for dftab (color shading or proportional size).
symbol: the type of symbol (square or circle).
center: a center value for method size.
centerpar: a logical or a list to represent center value using elements in the adegpar("ppoints") list.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

breaks.update: a logical indicating if the legend breaks is updating.

Call

an object of class call

Extends

Class ADEg.T, directly.
Class ADEg, by class ADEg.T, distance 2.
Class ADEgORtrellis, by class ADEg.T, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.T, distance 3.

Methods

The methods of the father classes "ADEg.T" and "ADEg" can be used by inheritance. The specific methods for T.value are:

prepare: signature(object = "T.value"): calls the parent method (prepare for ADEg.T) and modifies some graphical parameters used by default and calculates limits and grid.
panel: signature(object = "T.value"): draws symbols.

Note

For the symbol size, if the method is size, we use perceptual scaling (Tanimura et al. 2006) .

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Tanimura, S. and Kuroiwa, C. and Mizota, T. 2006 Proportional symbol mapping in R Journal of Statistical Software 15, 1–7

Examples

showClass("T.value")

Class `Tr.class`

Description

A class for group representation in triangular plot.

Objects from the Class

Tr.class objects can be created by calls of the form new("Tr.class", ...).

The regular usage in this package is to use the triangle.class function.

Slots

data

a list containing data or data's name.

dfxyz: the displayed values in the form of a data frame with three columns, a name or a matching call.
fac: a factor partitionning the rows of dfxyz.
wt: a vector of weights for fac.
labels: a vector containing the class' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.Tr class. The specific slots for Tr.class objects are:

ellipseSize: a positive number for ellipse size.
starSize: a number between 0 and 1 for star size.
chullSize: NULL or a vector of numbers between 0 and 1 for the convex hulls.
col: a NULL value, a color or a colors vector to color points, ellipses, labels, lines and polygons.
max3d and min3d: vectors of three values for triangular maximal and minimal limits.
adjust: a logical to adjust the device with the limits of the smaller equilateral triangle containing the values.

stats

a list of internal preliminary calculations. The specific slots for S2.class objects are:

means: a matrix containing the weighted mean calculated for each fac value.
mean2d: a matrix containing the weighted mean calculated for each fac value on two-dimension.
covvar: a list containing the weighted variance-covariance matrices calculated for each fac value.
covvar2d: a list containing the weighted variance-covariance matrices calculated for each fac value on two-dimension.

s.misc

a list of some others internal parameters:

ellipses: ellipses' coordinates.
chullcoord: convex hulls' coordinates.

Call

an object of class call

Extends

Class ADEg.Tr, directly.
Class ADEg, by class ADEg.Tr, distance 2.
Class ADEgORtrellis, by class ADEg.Tr, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.Tr, distance 3.

Methods

The methods of the father classes "ADEg.Tr" and "ADEg" can be used by inheritance. The specific methods for Tr.class are:

prepare: signature(object = "Tr.class"): calls the parent method (prepare for ADEg.Tr), modifies some graphical parameters used by default and calculates ellipses, convex hulls and centroids.
panel: signature(object = "Tr.class"): draws arrows, labels and points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("Tr.class")

Class `Tr.label`

Description

A class for creating and drawing triangular plot with point label.

Objects from the Class

Tr.label objects can be created by calls of the form new("Tr.label", ...).

The regular usage in this package is to use the triangle.label function.

Slots

data

a list containing data or data's name.

dfxyz: the displayed values in the form of a three columns data frame, a name or a matching call.
labels: a character vector containing labels for points.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.Tr class. The specific slots for Tr.class objects are:

addmean: a logical to plot the mean.
addaxes: a logical to draw the principal axes.
meanpar: a list to represent mean points using pch, cex and col.
axespar: a list to represent axes lines using col, lwd and lty.
max3d and min3d: vectors of three values for triangular maximal and minimal limits.
adjust: a logical to adjust the device with the limits of the smaller equilateral triangle containing the values.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters:

cornerp: coordinates of the triangle extremities.

Call

an object of class call

Extends

Class ADEg.Tr, directly.
Class ADEg, by class ADEg.Tr, distance 2.
Class ADEgORtrellis, by class ADEg.Tr, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.Tr, distance 3.

Methods

The methods of the father classes "ADEg.Tr" and "ADEg" can be used by inheritance. The specific methods for Tr.label are:

prepare: signature(object = "Tr.label"): calls the parent method (prepare for ADEg.Tr), modifies some graphical parameters used by default and defines the mean point and the axes.
panel: signature(object = "Tr.label"): draws lines, labels and points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("Tr.label")

Class `Tr.match`

Description

A class for the creation and display of paired coordinates in a triangular plot.

Objects from the Class

Tr.match objects can be created by calls of the form new("Tr.match", ...).

The regular usage in this package is to use the triangle.match function.

Slots

data

a list containing data or data's name.

dfxyz: the displayed values in the form of a three columns data frame, a name or a matching call.
labels: a vector of character strings containing the matches' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.Tr class. The specific slots for Tr.match objects are:

max3d and min3d: vectors of three values for triangular maximal and minimal limits.
adjust: a logical to adjust the device with the limits of the smaller equilateral triangle containing the values

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.Tr, directly.
Class ADEg, by class ADEg.Tr, distance 2.
Class ADEgORtrellis, by class ADEg.Tr, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.Tr, distance 3.

Methods

The methods of the father classes "ADEg.Tr" and "ADEg" can be used by inheritance. The specific methods for Tr.match are:

prepare: signature(object = "Tr.match"): calls the parent method (prepare for ADEg.Tr) and modifies some graphical parameters used by default.
panel: signature(object = "Tr.match"): draws arrows, labels and points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("Tr.match")

Class `Tr.traject`

Description

A class for the creation and display of triangular plot with trajectories linking the points.

Objects from the Class

Tr.traject objects can be created by calls of the form new("Tr.traject", ...).

The regular usage in this package is to use the triangle.traject function.

Slots

data

a list containing data or data's name.

dfxyz: the displayed values in the form of a three columns data frame, a name or a matching call.
fac: a factor (or a matrix of factors) splitting the rows of dfxyz.
labels: a vector of character strings containing the trajectories' labels.
frame: a positive or null integer. It is the number of the frame containing the data (used with sys.frame(..., env = data$frame)). Only if the data are not stored (i.e. data$storeData = FALSE).
storeData: a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored.

trellis.par

a list of parameters for lattice call. It will be passed directly to par.settings arguments of the lattice function.

adeg.par

a list of graphical parameters, corresponding to the ones given by adegpar() function.

lattice.call

a list to create the trellis object.

g.args

a list containing some method parameters linked with the created object of ADEg.Tr class. The specific slots for Tr.traject objects are:

max3d and min3d: vectors of three values for triangular maximal and minimal limits.
adjust: a logical to adjust the device with the limits of the smaller equilateral triangle containing the values
order: a vector containing the drawing order of the trajectories. A vector of length equal to factor.
col: a NULL value, a color or a colors vector to color points, labels and lines.

stats

a list of internal preliminary calculations

s.misc

a list of some others internal parameters

Call

an object of class call

Extends

Class ADEg.Tr, directly.
Class ADEg, by class ADEg.Tr, distance 2.
Class ADEgORtrellis, by class ADEg.Tr, distance 3.
Class ADEgORADEgSORtrellis, by class ADEg.Tr, distance 3.

Methods

The methods of the father classes "ADEg.Tr" and "ADEg" can be used by inheritance. The specific methods for Tr.traject are:

prepare: signature(object = "Tr.traject"): calls the parent method (prepare for ADEg.Tr) and modifies some graphical parameters used by default.
panel: signature(object = "Tr.traject"): draws arrows, labels and points.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

showClass("Tr.traject")

Superpose an new `ADEg` graph to the previous ones plotted

Description

Adds an ADEg to the current ADEg or ADEgS plot.

Usage

add.ADEg(object)

Arguments

object

an ADEg object

Details

This function uses the last plotted ADEg or ADEgS object.
It calls superpose.

Value

an ADEgS object

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

df1 <- cbind(rnorm(24), rnorm(24))
df2 <- cbind(rnorm(24), rnorm(24))
g1 <- s.label(df1, ppoints.col = "blue")
g2 <- s.label(df2, ppoints.col = "red", plot = FALSE)
add.ADEg(g2)

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g5 <- s.label(pca1$li, plabels.optim = TRUE)
g6 <- s.class(pca1$li, jv73$fac.riv, starSize = 0, ellipseSize = 0, chullSize = 1, 
  ppolygons.alpha = 0.4, col = rainbow(12), ppoints.cex = 0, plot = FALSE)
add.ADEg(g6)

Adds histograms and density lines against a bi-dimensional graphics.

Description

Adds the two marginal histograms and density lines of each axis against an ADEg.S2 object.

Usage

addhist(object, bandwidth, gridsize = 60, kernel = "normal", cbreaks = 2, 
  storeData = TRUE, plot = TRUE, pos = -1, ...)

Arguments

object

an ADEg.S2 object

bandwidth

used for the calculations of the density lines (see the bkde function of the KernSmooth package).

gridsize

used for the calculations of the density lines (see the bkde function of the KernSmooth package).

kernel

used for the calculations of the density lines (see the bkde function of the KernSmooth package).

cbreaks

number of cells for the histograms per interval of the grid of the bi-dimensional graphics.

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

Additional graphical parameters (see adegpar and trellis.par.get)

Details

Density is calculated using the function bkde of the KernSmooth package.

Value

An ADEgS object, a list of four graphical objects, one ADEg.S2 and three trellis (from lattice). Their names are:

object

the ADEg.S2 object

densX

top histogram, a trellis object

densY

right histogram, a trellis object

link

corner graphics linking the two histograms, a trellis object

Note

Into the dots arguments, the usual parameters for the s.label can be given with the object key.

Trellis parameters are used for the three remaining graphics. plot.polygon handles the histogram aspect, add.line the graduations lines and plot.line the density lines.

Finally, for the link graphic, labels aspect can be changed using a plabels list, as for an S2.label object.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(rpjdl, package = "ade4")
coa1 <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
labli <- s.label(coa1$li)
g1 <- addhist(labli)
g2 <- addhist(labli, plabels.cex = 0, cbreaks = 3)
labco <- s.label(coa1$co)
g3 <- addhist(labco, plabels.cex = 0, cbreaks = 3)
update(g3, pbackground.col = "grey85")

Adds lines on graphics.

Description

Adds a trellis object containing one or several lines on one or several graphical objects.

Usage

addline(object, a = NULL, b = 0, h = NULL, v = NULL, plot = TRUE, ...)

Arguments

object

an object of class ADEg or ADEgS

a, b

coefficients of the line to be added, passed to the panel.abline function of the lattice package

h, v

numeric vectors giving locations respectively of horizontal and vertical lines to be added to the plot, in native coordinates, passed to the panel.abline function of the lattice package

plot

a logical indicating if the graphics is displayed

...

Other arguments. Additional graphical parameters (see the plines list in adegpar and trellis.par.get). If object is an ADEgS, the argument which identify which ADEg is/are used for superposition.

Value

An object of class ADEgS.

Author(s)

Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

# example extracted from the pedagogic file, here: http://pbil.univ-lyon1.fr/R/pdf/tdr65.pdf
data(monde84, package = "ade4")
dfX <- cbind.data.frame(lpib = log(monde84$pib), croipop = monde84$croipop)
dfY <- cbind.data.frame(lmorta = log(monde84$morta), lanal = log(monde84$anal + 1), 
  rscol = sqrt(100 - monde84$scol))
dfX0 <- ade4::scalewt(dfX)
dfY0 <- ade4::scalewt(dfY)
can1 <- cancor(dfX0, dfY0)
varcanoX <- dfX0 %*% can1$xcoef[,1]
varcanoY <- dfY0 %*% can1$ycoef[,1]
g1 <- s.label(cbind(varcanoY,varcanoX), labels = row.names(monde84), plabel.cex = 0.8, plot = FALSE)
addline(g1, 0, 1, plines.col = "red", plines.lwd = 0.5, plines.lty = 2)

Adds points on graphics.

Description

Adds a trellis object containing one or several points on one or several graphical objects.

Usage

addpoint(object, xcoord, ycoord, plot = TRUE, ...)

Arguments

object

an object of class ADEg or ADEgS

xcoord

an integer (or a vector) indicating where label is(are) plotted on the x-axis, passed to the panel.points function of the lattice package

ycoord

an integer (or a vector) indicating where label is(are) plotted on the y-axis, passed to the panel.points function of the lattice package

plot

a logical indicating if the graphics is displayed

...

Other arguments. Additional graphical parameters (see the ppoints list in adegpar and trellis.par.get). If object is an ADEgS, the argument which identify which ADEg is/are used for superposition.

Value

An object of class "ADEgS".

Author(s)

Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(deug, package = "ade4")
deug$cent[1]
g1 <- s1d.density(deug$tab[, 1], plot = FALSE)
addpoint(g1, xcoord = deug$cent[1], ycoord = 0, ppoints = list(col = "black",
  pch = "*", cex = 3))

Adds segments on graphics.

Description

Adds a trellis object containing one or several segments on one or several graphical objects.

Usage

addsegment(object, x0 = NULL, y0 = NULL, x1, y1, plot = TRUE, ...)

Arguments

object

an object of class ADEg or ADEgS

x0, y0

coordinates of points FROM which to draw, passed to the panel.segments function of the lattice package. See Details.

x1, y1

coordinates of points TO which to draw, passed to the panel.segments function of the lattice package. See Details.

plot

a logical indicating if the graphics is displayed

...

Details

x0, y0, x1 and y1 can be vectors. A line segment is drawn, for each i, between the point (x0[i], y0[i]) and the point (x1[i], y1[i]). The coordinate vectors will be recycled to the length of the longest.

Value

An object of class ADEgS.

Author(s)

Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(deug, package = "ade4")
g11 <- s1d.density(deug$tab[, 1], plot = FALSE)
g12 <- addsegment(g11, x0 = deug$cent[1], x1 = deug$cent[1], y0 = 0, y1 = 1, 
  plines = list(col = "grey30", lwd = 3))
g13 <- addsegment(g11, 
  x0 = deug$cent + seq(0, 1, length.out = length(deug$cent)), 
  x1 = deug$cent + seq(0, 1, length.out = length(deug$cent)), 
  y0 = 0, y1 = 1, 
  plines = list(col = 1:length(deug$cent), lty = 1:length(deug$cent)))
  
# example extracted from the pedagogic file, here: http://pbil.univ-lyon1.fr/R/pdf/tdr65.pdf
data(monde84, package = "ade4")
dfX <- cbind.data.frame(lpib = log(monde84$pib), croipop = monde84$croipop)
dfY <- cbind.data.frame(lmorta = log(monde84$morta), lanal = log(monde84$anal + 1), 
  rscol = sqrt(100 - monde84$scol))
dfX0 <- ade4::scalewt(dfX)
dfY0 <- ade4::scalewt(dfY)
can1 <- cancor(dfX0, dfY0)
varcanoX <- dfX0 %*% can1$xcoef[,1]
varcanoY <- dfY0 %*% can1$ycoef[,1]
g21 <- s.label(cbind(varcanoY,varcanoX), labels = row.names(monde84), plabel.cex = 0.8, 
  plot = FALSE)
g22 <- addsegment(g21, -1.25, -1.25, 1.25, 1.25, plines.col = "purple", plines.lwd = 1.5, 
  plines.lty = 2)

Adds labels on graphics.

Description

Adds a trellis object containing one or several labels on one or several graphical objects.

Usage

addtext(object, xcoord, ycoord, label, plot = TRUE, ...)

Arguments

object

an object of class ADEg, trellis or ADEgS

xcoord

an integer (or a vector) indicating where label is(are) plotted on the x-axis, passed to the adeg.panel.label

ycoord

an integer (or a vector) indicating where label is(are) plotted on the y-axis, passed to the adeg.panel.label

label

a character string (or a vector) containing the label(s) displayed on object

plot

a logical indicating if the graphics is displayed

...

Other arguments. Additional graphical parameters (see the plabels list in adegpar and trellis.par.get). If object is an ADEgS, the argument which identify which ADEg is/are used for superposition.

Value

An object of class ADEgS.

Author(s)

Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(dunedata, package = "ade4")
afc1 <- ade4::dudi.coa(dunedata$veg, scannf = FALSE)
g1 <- table.value(dunedata$veg, symbol = "circle", ppoints.cex = 0.5, plot = FALSE)
addtext(g1, 1, 20, "A", plabels.srt = 45, plabels.box.draw = FALSE, plabels.col = "red")

xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
posi <- factor(xy$x > 0) : factor(xy$y > 0)
g2 <- s.class(xy, fac = posi, facets = posi, pellipses.col = 1:4, plabels.cex = 0, 
  plegend.drawKey = FALSE, psub.cex = 0, plot = FALSE)
addtext(g2, c(0.5, 0.5, -0.5, -0.5), c(0.5, -0.5), levels(posi), plabels.cex = 2, plabels.col = 1:4)

Panel function for adding spatial objects.

Description

Panel function adapted from the Sp package for displaying all kind of spatial objects handled by Sp (for classes inherited from the superclass Spatial) into a trellis graphic (lattice package).

Usage

adeg.panel.Spatial(SpObject, sp.layout = NULL, col = 1, border = 1, lwd = 1, 
  lty = 1, alpha = 0.8, cex = 1, pch = 20, n = length(col), spIndex = 1, ...)

Arguments

SpObject

an object of class "SpatialPoints", "SpatialPointsDataFrame",
"SpatialPixels", "SpatialPixelsDataFrame", "SpatialGrid",
"SpatialGridDataFrame", "SpatialLines", "SpatialLinesDataFrame",
"SpatialPolygons" or "SpatialPolygonsDataFrame"

sp.layout

a list of layout items. See spplot for more information

col

background color (fill) of Spobject

border

border color

lwd

line width (border)

lty

line type (border)

alpha

background transparency of Spobject

cex

point size

pch

point type

n

if SpObject contains data, the _desired_ number of intervals splitting the data (using pretty).

spIndex

if the SpObject contains a data frame, its values are represented with a color code. Only the spIndex data frame is represented

...

for coherence with panel functions

Value

Draws the Spatial object and layout.

Note

If SpObject contains several maps, only the first one is selected. Also for objects containing more data (for classes data.frame with a slot data), this information is also shown. To do so, various colors can be used (according to the col arguments).

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Package Sp. Author: Edzer Pebesma, Roger Bivand, Barry Rowlingson and Virgilo Gomez-Rubio.

Examples


if(require(lattice, quietly = TRUE) & require(sp, quietly = TRUE)) {
data(elec88, package = "ade4")

xy <- elec88$xy
arrow <- list("SpatialPolygonsRescale", offset = c(150000,1700000),
layout.north.arrow(), scale = 100000)

xyplot(xy[, 2] ~ xy[, 1], aspect = "iso", panel = function(...){
  adeg.panel.Spatial(SpObject = elec88$Spatial, sp.layout = list(arrow), 
  col = colorRampPalette(c("yellow", "blue"))(5), border =
  "transparent")})
}

Panel function for adding histograms.

Description

Panel function for displaying histograms into a trellis graphic (lattice package) and level lines.

Usage

adeg.panel.hist(histValues, horizontal = TRUE, densi, drawLines, params = list(), 
  identifier = "histogramADEg")

Arguments

histValues

an object of class histogram. See hist.

horizontal

a logical indicating if the plot is horizontal

densi

a list returns by the bkde containing the coordinates of the binned kernel density estimate of the probability density of the data

drawLines

a vector containing the level values

params

graphical parameters : plot.polygon, add.line and plot.line (lattice)

identifier

A character string that is prepended to the name of the grob that is created.

Value

Displays the histogram and level lines.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

if(require(KernSmooth, quietly = TRUE) & require(lattice, quietly = TRUE)) {

  z <- round(rnorm(100, 30, 5))
  h <- hist(z, plot = FALSE)
  d <- bkde(z, kernel = "normal", gridsize = 60)
  l <- c(10, 20, 30, 40)
  xyplot(1:50 ~ 1:50, histValues = h, densi = d, drawLines = l, 
    panel = function(drawLines, histValues, densi){
      adeg.panel.hist(histValues = histValues, drawLines = drawLines, densi = densi)})
}

Panel function for joining lines.

Description

Panel function for drawing lines as part of a circle centred in (0, 0) into a trellis graphic (lattice package).

Usage

adeg.panel.join(drawLines, params = list())

Arguments

drawLines

a vector containing the level values used as radius of the circle

params

graphical parameters : plabels and add.line (lattice)

Value

Displays level lines and their values.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

if(require(lattice, quietly = TRUE)) {
  xyplot(0:20 ~ 0:20, drawLines = c(5, 10, 15), params = list(plabels.cex = 2), 
    panel = function(drawLines, params){
      adeg.panel.join(drawLines = drawLines, params = params)})
}

Panel function for adding labels.

Description

Panel function for drawing labels into a trellis graphic (lattice package) with or without boxes around labels.

Usage

adeg.panel.label(x, y, labels, plabels, pos = NULL)

Arguments

x

a numeric vector, x-coordinates for the labels

y

a numeric vector, y-coordinates for the labels

labels

a vector of character string, the labels

plabels

a list of parameters as an extract of adegpar("plabels"), used for labels' drawing. Each value can be a vector and will be recycled if necessary:

alpha, cex, col: drawing parameters for the text
srt: orientation of the labels, horizontal, vertical or an angle indication (in degrees). Boxes are not rotated. If the orientation is not near to horizontal/vertical (0/90), it is best not to draw the boxes
optim: logical. If TRUE, uses an algorithm trying to avoid labels' overlapping and outside limits
boxes: concerns the label's boxes. a list:
- draw: logical. If TRUE, labels are framed
- alpha, border, col, lwd, lty: rule transparency, border lines and background color

pos

a position specifier for the text, used in panel.text. Values of 1, 2, 3 and 4 respectively indicate positions below, to the left of, above and to the right of the specified coordinates.

Value

Draws the labels.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

The algorithm used for labels positions optimization is inspired by the pointLabel function of the car package (since 2022-10-22, moved from the the maptools package, developed by Tom Short).

Examples

if(require(lattice, quietly = TRUE)) {
param <- adegpar("plabels")[[1]]
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.label(x, y, LETTERS[1:10], plabels = param)})
}

if(require(lattice, quietly = TRUE)) {
param$boxes$draw <- FALSE
param$col <- "blue"
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.label(x, y, LETTERS[1:10], plabels = param)})
}

Panel functions for adding graphs.

Description

Panel function for representing a graph into a trellis graphic (lattice package).
Two types of graph objects can be used: nb or listw object (spdep package) or simple edges informations.
Directions associated with the edges are not displayed.

Usage

adeg.panel.nb(nbobject, coords, col.edge = "black", lwd = 1, lty = 1, pch = 20, 
  cex = 1, col.node = "black", alpha = 1)

adeg.panel.edges(edges, coords, col.edge = "black", lwd = 1, lty = 1, pch = 20, 
  cex = 1, col.node = "black", alpha = 1)

Arguments

nbobject

a object of class nb or listw

edges

a two columns matrix, representing the edges between the nodes. For a row i, x[i, 1] and x[i, 2] are linked, x[i, 1] and x[i, 2] being vertices number.

coords

a two columns matrix containing vertices' coordinates

col.edge

edges' color(s)

lwd

line width (edges). Can be a vector

lty

line type (edges). Can be a vector

pch

vertices' representation type (symbols). Can be a vector

cex

symbols' size(s) (vertices). Can be a vector

col.node

vertices' color(s). Can be a vector

alpha

symbols' transparency

Value

Displays the neighboring graph.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Package spdep. Author: Roger Bivand

Examples

if(require(lattice, quietly = TRUE) &
  require(spdep, quietly = TRUE)) {

  data(elec88, package = "ade4")
  coords <- elec88$xy
  xyplot(coords[, 2] ~ coords[, 1],
    panel = function(...){adeg.panel.nb(elec88$nb, coords, col.edge = c("blue", "red"))})
}

if(require(lattice, quietly = TRUE)) {
  edges <- matrix(c(1, 2, 3, 2, 4, 1, 3, 4), byrow = TRUE, ncol = 2)
  coords <- matrix(c(0, 1, 1, 0, 0, -1, -1, 0), byrow = TRUE, ncol = 2)
  xyplot(coords[,2] ~ coords[,1],
    panel = function(...){adeg.panel.edges(edges, coords, lty = 1:4, cex = 5)})
}

Panel function drawing a third variable into a two-dimensional scatterplot

Description

Panel function for drawing coordinates with variable representation. The values can be represented through symbols with proportional size or various colors.

Usage

adeg.panel.values(x, y, z, method, symbol, ppoints, breaks, centerpar = NULL, 
  center = 0)

Arguments

x

a numeric vector, x-coordinates for the symbols

y

a numeric vector, y-coordinates for the symbols

z

a numeric vector, the third variable with one value per coordinates (x, y)

method

a character string equal to color or size.
If color, a palette of color is used for the symbols (one color per interval defined by breaks).
If size, symbols' area is proportional to the value. Area is 0 for values equals to center. Two colors are used, one for values smaller than center and the other for values larger than center.

symbol

a character string equal to square or circle.

ppoints

a list of parameters as an extract of adegpar("ppoints"), used for points' drawing.

alpha: transparency of points
cex: size of points
col: border color of points
pch: symbol to use
fill: filling color

breaks

a vector, the breaks used for splitting z if method is color

centerpar

a list to represent center value using elements in the adegpar("ppoints") list or NULL value. If the method is size, z-values equals to center have a size of zero. If centerpar is not NULL, those z-values are shown as points with the centerpar drawing parameters.

center

a center value for method size

Value

Draws the points.

Note

For more information about the use of panel functions, please see the lattice package developed by Deepayan Sarkar.

For the symbols size, the method is size uses perceptual scaling (Tanimura et al. 2006).

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Tanimura, S. and Kuroiwa, C. and Mizota, T. 2006 Proportional symbol mapping in R Journal of Statistical Software 15, 1–7

Examples

if(require(lattice, quietly = TRUE)) {
param <- adegpar("ppoints")[[1]]
param$col <- adegpar("ppalette")[[1L]]$quanti(2)
z <- rnorm(10)
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.values(x, y, z, method = "size", symbol = "square", ppoints =
  param, breaks = pretty(z, 4))})
}

if(require(lattice, quietly = TRUE)) {
param$col <- adegpar()$ppalette$quali((length(pretty(z, 2)) - 1))
xyplot(1:10 ~ 1:10, panel = function(x, y, ...){
  adeg.panel.values(x, y, z, method = "color", symbol = "circle", 
                    ppoints = param, breaks = pretty(z, 2))}) 
}

Handling ADEg graphical parameters

Description

adegpar can be used to set or query graphical parameters used in ADEg object display.

It is inspired by the par function of graphics package.

Usage

adegpar(...)

Arguments

...

If it is empty, the return value is a named list containing all the current settings.

If it is a string of characters, the corresponding sub-list of parameters is return as information.

If it is a list containing keys and values, the corresponding changes in current settings are made.

Details

The graphical parameters control apparency of the graphic. Calls can be made using either a list of list (e.g. plabels = list(col = "red")) or a list grouping both keys with "." (e.g. plabels.col = "red").

Parameters are re-used if needed in all ADEg object. If set globally, meaning using adegpar, all created objects afterwards will be affected.

Value

Several parameters are used to create complete plot and accessible through adegpar.

p1d:

parameters for one-dimension graphic, object of class inherited from "ADEg.S1" or "ADEg.C1"

horizontal: a logical indicating if the plot is horizontal
reverse: a logical indicating if the bottom of the plot is at the bottom (for horizontal as TRUE) or at the left of the device (for horizontal as FALSE). If FALSE, the graphical display bottom is at the top (for horizontal as TRUE) or at the right of the device (for horizontal as FALSE).
rug: a list dedicated to tick marks
- draw: a logical indicating if the rugs are drawn
- tck: size of the rug (ticks) in proportion from the reference line and the origin of the device (0.5 by default)
- margin: where to draw the reference line (0.07 by default)
- line: a logical indicating if the reference line is drawn using porigin arguments

parrows:

arrows' parameters. see panel.arrows for more information

angle: angle from the shaft of the arrow to the edge of the arrow head
ends: kind of arrows to be drawn. Can be first, last or both
length: length of the edges of the arrow head

paxes:

axis' parameters. Mostly inspired by xyplot function of lattice package

aspectratio: a character string to control physical aspect ratio of the graphic (drawing panel more specifically). iso for isometric scales, fill for drawing as big as possible or xy for banking rule
draw: a logical indicating if axis (tick marks and labels) are drawn around the graphic
x: a list used for the creation of x-axis in the trellis object. See xyplot for more information
- draw: a logical indicating if x-axis (tick marks and labels) are drawn around the graphic
y: the same list as for x with draw parameters

pbackground:

background's parameters

col: background color
box: a logical indicating if a box is drawn surrounding the plot

pellipses:

ellipses' drawing parameters

alpha: a value between 0 and 1 controlling ellipses' background transparency
axes: a list dedicated to ellipses' axis
- draw: a logical indicating whether ellipses' axis are drawn
- col: ellipses' axis color
- lty: line type of ellipses' axis
- lwd: line width of ellipses' axis
border: ellipses's border color
lty: line type of ellipses' border
lwd: line width of ellipses' border
col: ellipses' background color

pgrid:

grid's drawing parameters

draw: a logical indicating if grid is drawn in the background
col: grid's line color
lty: line type of grid line
lwd: line width of grid line
nint: an integer indicating the number of grid intervals expected
text: a list dedicated to grid legend text
- cex: text size of grid legend
- col: text color of grid legend
- pos: a character string (topright, topleft, bottomleft, bottomright) or a vector of length 2 indicating text position of grid legend. If it is a vector, the default unit is npc (normalized parent coordinates).

plabels:

labels' drawing parameters

alpha: a value between 0 and 1 controlling label transparency
cex: labels' text size
col: labels' text color
srt: labels' text orientation. It can be horizontal, vertical or an angle indication in degrees
optim: a logical indicating if an algorithm is used to avoid labels' overlapping or outside limits
boxes: label's boxes parameters
- draw: a logical indicating if labels are framed
- alpha: a value between 0 and 1 controlling labels' boxes transparency
- border: boxes' border color
- col: boxes' background color
- lty: line type of boxes' border
- lwd: line width of boxes' border

plegend:

legend's drawing parameters (used for object of class inherited from T.value and S2.value)

drawKey: a logical indicating if the legend should be drawn. Legend can be provided by the key argument or is automatically generated for *.class and *.value functions
drawColorKey: a logical indicating if the color legend should be drawn (only for *.image functions)
size: size of the legend

plines:

lines' drawing parameters

col: lines color
lty: lines type
lwd: lines width

pnb:

drawing parameters for neighbourhood graph

edge: edge's drawing parameters
- col: edge color
- lty: line type of edge
- lwd: line width of edge
node: node's drawing parameters
- pch: node's symbol type
- cex: node's symbol size
- col: node's symbol color
- alpha: a value between 0 and 1 controlling node's symbol transparency

porigin:

drawing parameters for origin's lines. See panel.lines for more information

draw: a logical indicating if vertical and horizontal lines are drawn to indicate origin
include: a logical indicating if origin is included in the drawing limits
origin: a two-length vector indicating origin coordinates
alpha: a value between 0 and 1 controlling origin's lines transparency
col: color of origin's lines
lty: origin's line type
lwd: origin's line width

ppalette:

a function taking one integer in argument indicating the number of expecting colors (for example using colorRampPalette)

quanti: adegpar()$ppalette$quanti(n) returns n colors shaded grey to white
quali: adegpar()$ppalette$quali(n, name) returns n differentiated colors. name argument is passed to the brewer.pal function of the RColorBrewer package and must be Accent, Dark2, Paired, Pastel1, Pastel2, Set1 (the default value), Set2 or Set3. When n is equal to 2, values for 'white' and 'black' colors are returned and can be not quite visible on the display.

ppoints:

points' drawing paameters

alpha: a value between 0 and 1 controlling points transparency
cex: points size
col: points color
pch: points type
fill: points' background color (only for filled points type)

ppolygons:

polygons' drawing parameters (used for example to draw convex hull for S2.class or Gaussian curves for C1.gauss objects). See lpolygon for more information.

border: polygon's border color
col: polygon's background color
lty: line type of polygon border
lwd: line width of polygon border
alpha: a value between 0 and 1 controlling polygons' background transparency

pSp:

drawing parameters for spatial object

col: spatial object's background color
border: spatial object's border color
lty: line type of spatial object border
lwd: line width of spatial object border
alpha: a value between 0 and 1 controlling spatial object transparency

psub:

subtitle's drawing parameters

cex: text size of subtitle
col: text color of subtitle
position: a character string (topright, topleft, bottomleft, bottomright) or a vector of length 2 indicating text position of subtitle. If it is a vector, the default unit is npc (normalized parent coordinates).
text: the character string to display

ptable:

for table graphic, object of class inherited from ADEg.T

x: x-axis parameters
- srt: text rotation
- pos: position of the axis. It can be top or bottom. Otherwise axis and labels' axis are not drawn
- tck: ticks size
- adj: justification of labels
y: same as x list, but for y-axis
- str, tck, adj
- pos: position of the axis. It can be left or right. Otherwise axis and labels' axis are not drawn
margin: margin surrounding the drawing panel. The numbers indicate the bottom, left, top and right margins. Results are obtained passing margin to padding argument in lattice. Please see layout.heights and layout.widths parameters in lattice package for more information

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

oldparamadeg <- adegpar()
    
X <- data.frame(x = runif(50, -1, 2), y = runif(50, -1, 2))
s.label(X)
names(adegpar())
adegpar("paxes.draw", "psub.cex")
adegpar()$pback$col
adegpar("paxes.draw" = TRUE, "psu.ce" = 3, "pback.col" = "grey85")
s.label(X)

adegpar(oldparamadeg)

Combine `ADEg` objects by columns or rows

Description

Take a sequence of ADEg, ADEgS or trellis arguments and combine by columns or rows, respectively.

Usage

cbindADEg(g1, g2, ..., plot = FALSE)
rbindADEg(g1, g2, ..., plot = FALSE)

Arguments

g1

an object of class ADEg, ADEgS or trellis

g2

an object of class ADEg, ADEgS or trellis

...

other objects of class ADEg, ADEgS or trellis

plot

a logical indicating if the graphics is displayed

Value

an ADEgS object

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g1 <- s.label(pca1$li, plabels.optim = TRUE, plot = FALSE)
g2 <- s.class(pca1$li, jv73$fac.riv, starSize = 0, ellipseSize = 0, chullSize = 1, 
  ppolygons.alpha = 0.4, col = rainbow(12), ppoints.cex = 0, plot = FALSE)
g3 <- s.corcircle(pca1$co, pbackground.box = FALSE, plot = FALSE)
g4 <- rbindADEg(cbindADEg(g1, g2), cbindADEg(superpose(g1, g2), g3), plot = TRUE)

Change the `lattice` theme used for `adegraphics`

Description

This function allows to modify the default theme existing for adegraphics objects. The created theme also affects previously created objects.

Usage

changelatticetheme(...)

Arguments

...

lattice parameters, the same used in trellis.par.set and provided by trellis.par.get. If empty, reset the theme to the adegraphics one.

Note

The adegraphics theme removes all margins, sets a transparent background and grey regions.

A further development will be the creation of various themes for adegraphics.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

if(require(lattice, quietly = TRUE)) {
  show.settings()
  changelatticetheme(list(superpose.symbol = list(pch = c(21, 22, 35), cex = 1)))
  show.settings()
  show.settings()[1]
}

Method for `ADEg` and `ADEgS` objects

Description

getcall returns the call used to create the object.

Methods

signature(object = "ADEg"): returns the slot Call of the object ADEg
signature(object = "ADEgS"): returns the slot Call of the object ADEgS

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Insert a graphic into an existing one

Description

This function inserts a first graphic into a previously created and/or a displayed one.

Usage

insert(graphics, oldgraphics, posi = c("bottomleft", "bottomright", "topleft", 
  "topright"), ratio = 0.2, inset = 0.0, plot = TRUE, which, dispatch = FALSE)

Arguments

graphics

an object of class ADEg, ADEgS or trellis

oldgraphics

an object of class ADEg, ADEgS or missing. If oldgraphics is missing, graphics is added on the current device.

posi

a character value or a two-length numeric vector (in normalized parent coordinates npc from 0 to 1) indicating the position of olgraphics added into graphics

ratio

a numeric value from 0 to 1 indicating the size of olgraphics regarding the plot region

inset

the inset from which the graph is drawn regarding the plot region. It can be a two-length vector giving the inset in x and y. If atomic, same inset is used in x and y.

plot

a logical indicating if the graphics is displayed

which

a numeric value or a vector of values only used if oldgraphics is an ADEgS object, indicating the which-th sub-graphic of oldgraphics where graphics is added.

dispatch

a logical only used if both graphics and oldgraphics are ADEgS objects with same length, indicating if graphics is added one by one int oldgraphics. It is used when both graphics and oldgraphics are created with facets option.

Value

An object of class "ADEgS".

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(deug, package = "ade4")
dd1 <- ade4::dudi.pca(deug$tab, scannf = FALSE, nf = 4)
g1 <- s.label(dfxy = dd1$li, labels = rownames(dd1$li), plabels = list(cex = 0.75), plot = FALSE)
g2 <- s1d.barchart(score = dd1$eig, plot = FALSE, 
  ppolygons = list(col = c(rep("black", 2), rep("grey", 2), rep("white", 5))), 
  p1d = list(horizontal = FALSE), psub = list(position = "topright", text = "Eigenvalues"), 
  pgrid = list(draw = FALSE), pbackground = list(box = TRUE), xlim = c(0.5, 9.5))
g1
g3 <- insert(g2, plot = FALSE)

mat <- g3@positions
mat[2, ] <- c(0.8, 0, 1, 0.2)
update(g3, positions = mat, plot = FALSE)
print(g3) ## square == NULL
print(g3, square = TRUE)
print(g3, square = FALSE)

g4 <- insert(g2, g1, posi = "topleft")

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g5 <- s.value(jv73$xy, pca1$li[, 1:2], porigin.include = FALSE, plot = FALSE)
g6 <- s.corcircle(pca1$co, pbackground.box = FALSE, plot = FALSE)
g7 <- insert(g6, g5, posi = c(0.3, 0.4, 0.5, 0.6))

For internal use only

Description

Internal classes, methods and functions. Not for users.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Transform a layout matrix into a position one

Description

This function transforms layout's informations into a position matrix useful for ADEgS and for lattice graphics.

Usage

layout2position(mat, widths = rep(1, NCOL(mat)), heights = rep(1, NROW(mat)), ng, 
square = FALSE)

Arguments

mat

a matrix indicating the location of figures to display (each value must be 0 or a positive integer) or a two-length vector indicating the number of rows and columns in the corresponding layout.

widths

a vector of relative values for the columns' widths on the device. Their sum must be equal to the number of columns.

heights

a vector of relative values for the rows' heights on the device. Their sum must be equal to the number of rows.

ng

a value for the number of positions needed (i.e. the number of graphics to plot)

square

a logical indicating if the graphics is an isometric plot

Value

A four-columns matrix indicating the coordinates (in normalized parent coordinates npc) of the top-right and bottom-left hand corners of each displayed figure on the device.

Note

This function is strongly inspired by the layout function in graphics package.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

layout2position(mat = rbind(c(0, 0, 1), c(2, 2, 1)))
layout2position(mat = cbind(c(0, 0, 1), c(2, 2, 1)), widths = c(0.5, 1.5))

Methods `panel` for `ADEg` objects

Description

The method panel displays all specific graphical components.

Methods

signature(object = "C1.barchart"): draws bar charts and labels
signature(object = "C1.curve"): draws points and curves
signature(object = "C1.curves"): draws multiple points and curves
signature(object = "C1.density"): draws density curves
signature(object = "C1.dotplot"): draws segments and dots
signature(object = "C1.gauss"): draws Gauss curves and level names of each curve
signature(object = "C1.hist"): draws rectangles
signature(object = "C1.interval"): draws segments or polygons
signature(object = "S1.boxplot"): draws box-and-wiskers diagrams, mean points and labels
signature(object = "S1.class"): draws labels and lines matching with score values
signature(object = "S1.distri"): draws mean points and segments with matching labels
signature(object = "S1.label"): draws labels and its links with score points
signature(object = "S1.match"): draws score points and matching segments and labels
signature(object = "S2.arrow"): draws points, arrows and labels
signature(object = "S2.class"): draws ellipses, convex hulls, stars, labels and points
signature(object = "S2.corcircle"): draws arrows, labels and axes
signature(object = "S2.density"): draws densities and external points
signature(object = "S2.distri"): draws ellipses, stars, labels and points
signature(object = "S2.image"): draws raster image
signature(object = "S2.label"): draws points and labels
signature(object = "S2.logo"): displays the logos
signature(object = "S2.match"): draws arrows and labels
signature(object = "S2.traject"): draws points, arrows and labels
signature(object = "S2.value"): draws symbols
signature(object = "T.cont"): draws mean points and regression lines
signature(object = "T.image"): draws raster image
signature(object = "T.value"): draws symbols
signature(object = "Tr.class"): draws arrows, labels and points
signature(object = "Tr.label"): draws lines, labels and points
signature(object = "Tr.match"): draws arrows, labels and points
signature(object = "Tr.traject"): draws arrows, labels and points

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Methods to display the outputs of an analysis performed with `ade4`

Description

S3 methods to display the outputs of an analysis performed with ade4

Usage

## S3 method for class 'foucart'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), pos = -1, 
  storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mcoa'
kplot(object, xax = 1, yax = 2, which.tab = 1:nrow(object$cov2), 
  option = c("points", "axis", "columns"), pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mfa'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), traject = FALSE, 
  permute = FALSE, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mbpcaiv'
kplot(object, xax = 1, yax = 2, which.tab =
1:length(object$blo), pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pta'
kplot(object, xax = 1, yax = 2, which.tab = 1:nrow(object$RV), which.graph = 1:4, 
  pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'sepan'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), permute = FALSE, 
  traject = FALSE, posieig = "bottomleft", pos = -1, storeData = TRUE, plot = TRUE, ...)
kplotsepan.coa(object, xax = 1, yax = 2, which.tab = 1:length(object$blo), 
  permute = FALSE, posieig = "bottomleft", pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'statis'
kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$tab.names), traject = FALSE, 
  arrow = TRUE, class = NULL, pos = -1, storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'acm'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betcoi'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betdpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betwitdpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'betrlq'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'between'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'coinertia'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'discrimin'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'dpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'fca'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'foucart'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'krandboot'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'krandxval'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mfa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE,
plot = TRUE, ...)
## S3 method for class 'multiblock'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'multispati'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'niche'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pcaiv'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pta'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'procuste'
plot(x, xax = 1, yax = 2, pos = -1, storeData =
TRUE, plot = TRUE, ...)
## S3 method for class 'randboot'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'randxval'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'rlq'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'sepan'
plot(x, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'statis'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witcoi'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witdpcoa'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'within'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'witrlq'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'bcaloocv'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'discloocv'
plot(x, xax = 1, yax = 2, pos = -1, storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'dudi'
scatter(x, xax = 1, yax = 2, permute = FALSE, posieig = "topleft", prop = FALSE, 
  density.plot = ifelse(permute, ncol(x$tab) > 1000, nrow(x$tab) > 1000), plot = TRUE, 
  storeData = TRUE, pos = -1, ...)
## S3 method for class 'coa'
scatter(x, xax = 1, yax = 2, method = 1:3, posieig = "topleft", pos = -1, 
  storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'pco'
scatter(x, xax = 1, yax = 2, posieig = "topleft", pos = -1, storeData = TRUE, 
  plot = TRUE, ...)
## S3 method for class 'nipals'
scatter(x, xax = 1, yax = 2, posieig = "topleft", pos = -1, storeData = TRUE, 
  plot = TRUE, ...)

## S3 method for class 'acm'
score(x, xax = 1, which.var = NULL, type = c("points", "boxplot"), pos = -1, 
  storeData = TRUE, plot = TRUE, ...)
## S3 method for class 'mix'
score(x, xax = 1, which.var = NULL, type = c("points", "boxplot"), pos = -1, 
  storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'pca'
score(x, xax = 1, which.var = NULL, pos = -1, storeData = TRUE, plot = TRUE, ...)

## S3 method for class 'dudi'
screeplot(x, col.kept = "grey", col = "white", pos = -1, plot = TRUE, ...)

## S3 method for class 'dudi'
biplot(x, pos = -1, plot = TRUE, ...)

Arguments

object, x

objects used to select a method

xax

an integer (or a vector) indicating which column(s) of object or x is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of object or x is(are) plotted on the y-axis

which.tab

a numeric vector (used in kplot.*) containing the numbers of the tables used for the analysis

option

a string of characters (only used in kplot.mfa) indicating the drawing option: points plot of the projected scattergram onto the co-inertia axes, axis projections of inertia axes onto the co-inertia axes, columns projections of variables onto the synthetic variables planes.

which.graph

an integer between 1 and 4 (only used in kplot.pta) indicating the drawing option. For each table of which.tab, are drawn: 1 the projections of the principal axes, 2 the projections of the rows, 3 the projections of the columns, 4 the projections of the principal components onto the planes of the compromise.

permute

a logical value (used in kplot.sepan, kplotsepan.coa and scatter.dudi). If FALSE, the rows are plotted by points or density surface and the columns by arrows. If TRUE, it is the opposite.

traject

a logical value (used in kplot.sepan and kplot.statis) indicating whether the trajectories between rows should be drawn in a natural order

posieig

a character value or a two-length numeric vector (in normalized parent coordinates npc from 0 to 1) or none value indicating the position of the eigenvalues bar plot (used in kplot.sepan, kplotsepan.coa and scatter.*).

arrow

a logical value (only used in kplot.statis) indicating whether the column factorial diagrams should be plotted

class

if not NULL, a factor of length equal to the number of the total columns of the K-tables (only used in kplot.statis)

prop

a logical value (only used in scatter.dudi) indicating if the size of the arrows' labels is proportional to the analysis score.

density.plot

a logical value (only used in scatter.dudi)indicating if the points are displayed as density surface (using s.density).

method

an integer between 1 and 3 (only used in scatter.coa) indicating the drawing option. Are drawn: 1 rows and columns with the coordinates of lambda variance, 2 rows variance 1 and columns by averaging, 3 columns variance 1 and rows by averaging.

which.var

the numbers of the kept columns for the analysis, otherwise all columns (used in score.*)

type

a string of characters (only used in score.acm and score.mix) indicating if points (points) or boxplot (boxplot) are used to represent levels of factors

col.kept

one color value to color the kept axes in the barchart (used in screeplot.dudi)

col

one color value to color the axes in the barchart (used in screeplot.dudi)

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

Returns an ADEg or an ADEgS object. The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

See ade4 website: <URL: http://pbil.univ-lyon1.fr/ADE-4/>

Examples

cat("To run the example on 'topic'\n")
cat("Type in your R console: example(topic, package = 'ade4') \n")

Display the decomposition of inertia which measure the contributions of rows/columns in mutivariate methods

Description

S3 method to display the decomposition of inertia (inertia object) which measure the contributions of rows/columns in mutivariate methods (dudi objects from ade4)

Usage

## S3 method for class 'inertia'
plot(x, xax = 1, yax = 2, threshold = 0.1, 
  contrib = c("abs", "rel"), type = c("label", "cross", "ellipse", "both"), 
  ellipseSize = 1.5, posieig = "none", plot = TRUE, 
  storeData = TRUE, pos = -1, ...)
## S3 method for class 'inertia'
score(x, xax = 1, threshold = 0.1, contrib = c("abs", "rel"), 
  posieig = "none", pos = -1, storeData = TRUE, plot = TRUE, ...)

Arguments

x

an object of the dudi class; it must be the output of a correspondance analysis (coa object).

xax

an integer indicating which column of x is plotted on the x-axis

yax

an integer indicating which column of x is plotted on the y-axis. If yax is equal to xax, a one-dimensional graph is display.

threshold

a numeric value containing the contribution threshold (between 0 and 1) at which points should be drawn on the graphic. Low contribution points will be represented by a grey point and without label. When the contributions are displayed on a single axis, a dotted line describes the contribution threshold.

contrib

a character value indicating which contributions are plotted: abs for absolute contributions (rows/columns involved in the factor axis/map construction) and rel for relative contribution (quality of rows/columns representation on the factor axis/map).

type

a character value indicating which type represents contribution. Labels size (label), crosses size(cross) or ellipses size (ellipse) can be proportional to the contributions. If type is both, crosses and ellipses both have sizes proportional to the contributions.

ellipseSize

a positive number for ellipse size when type is ellipse

posieig

a character value or a two-length numeric vector (in normalized parent coordinates npc from 0 to 1) or none value indicating the position of the eigenvalues bar plot.

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

Returns an ADEgS object. The result is displayed if plot is TRUE.

Author(s)

Clément Claustre, Anne-Béatrice Dufour, Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stéphane Dray

Examples

# First example
data(bf88, package = "ade4")
coa1 <- ade4::dudi.coa(bf88$S1, scannf = FALSE, nf = 3)

###### row=T / col=F
res11 <- ade4::inertia(coa1, row = TRUE, col = FALSE, nf = 3)
g111 <- plot(res11, threshold = 0.06)
g112 <- plot(res11, threshold = 0.06, xax = 1, yax = 3)
g12 <- plot(res11, threshold = 0.06, plabels.boxes.draw = TRUE, plines.lwd = 0,
  light_row.ppoints.cex = 0, posieig = "bottomleft")
g13 <- score(res11, threshold = 0.06)
names(g13)
g14 <- score(res11, xax = 2, threshold = 0.06)

###### row=F / col=T
res12 <- ade4::inertia(coa1, row = FALSE, col = TRUE, nf = 2)
res12$col.abs
idx <- which(res12$col.abs[, 1]/100 >= 0.1 | res12$col.abs[, 2]/100 >= 0.1)
rownames(res12$col.abs[idx, ])
coa1$co[idx, ]
g15 <- plot(res12)
g16 <- score(res12, threshold = 0.08)
g17 <- score(res12, threshold = 0.07)


########################################
########################################
# Second example
data(housetasks, package = "ade4")
coa2 <- ade4::dudi.coa(housetasks, scann = FALSE)

###### row=T / col=F
res21 <- ade4::inertia(coa2, row = TRUE, col = FALSE)
g21 <- plot(res21)
g22 <- score(res21)
g23 <- score(res21, xax = 2)

###### row=F / col=T
res22 <- ade4::inertia(coa2, row = FALSE, col = TRUE)
g24 <- plot(res22, plabels.cex = 2)
names(g24)
g25 <- plot(res22, posieig = "topleft")
names(g25)
g26 <- plot(res22, heavy_col.plabels.box.draw = TRUE, 
  light_col.ppoints.col = "purple")
g27 <- plot(res22, type = "both")
g28 <- plot(res22, type = "ellipse", ellipseSize = 3, plabels.col = "black", 
  pellipse.col = "purple", pellipses.border = "black")

Plot a barchart of eigen values

Description

This function represents a simplified barchart adapted to display eigen values. The bar color depends on whether the axis is displayed, kept or not.

Usage

plotEig(eigvalue, nf, xax = 1, yax = 2, col.plot = "black", col.kept = "grey", 
  col = "white", facets = NULL, plot = TRUE, storeData = FALSE, pos = -1, ...)

Arguments

eigvalue

a numeric vector of eigenvalues

nf

the number of retained factors, NULL if not provided

xax

an integer indicating which factor is plotted on the x-axis

yax

an integer indicating which factor is plotted on the y-axis

col.plot

a color value to fill the bar corresponding to the displayed factors

col.kept

a color value to fill the bar corresponding to the kept by not displayed factors

col

a color value to fill the bar corresponding to the other factors

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for bars are available in ppolygons of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.barchart).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

  data(microsatt, package = "ade4")
  w <- ade4::dudi.coa(data.frame(t(microsatt$tab)), scann = FALSE, nf = 3)
  g1 <- s.label(w$co, plot = FALSE)
  g2 <- plotEig(w$eig, w$nf, psub = list(text = "Eigenvalues"), pbackground = list(box = TRUE), 
    plot = FALSE)
  G <- insert(g2, g1, posi = "bottomright", ratio = 0.25)

Methods `prepare` for `ADEg` objects

Description

The method prepare performs the first calculus needed for the display.

Methods

signature(object = "ADEg.C1"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
signature(object = "C1.barchart"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default
signature(object = "C1.curve"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default
signature(object = "C1.density"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the density curves according to the numeric score and the values' categories
signature(object = "C1.dotplot"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default
signature(object = "C1.gauss"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the Gauss curves according to the numeric score and the values' categories (using weighted mean and standard deviation)
signature(object = "C1.hist"): calls the parent method (prepare for ADEg.C1), modifies some graphical parameters used by default and calculates the boundaries and the height of cells
signature(object = "C1.interval"): calls the parent method (prepare for ADEg.C1) and modifies some graphical parameters used by default
signature(object = "ADEg.S1"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
signature(object = "S1.boxplot"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default
signature(object = "S1.class"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default
signature(object = "S1.distri"): calls the parent method (prepare for ADEg.S1), modifies some graphical parameters used by default and calculates weighted mean and standard deviation
signature(object = "S1.label"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default
signature(object = "S1.match"): calls the parent method (prepare for ADEg.S1) and modifies some graphical parameters used by default
signature(object = "ADEg.S2"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
signature(object = "S2.arrow"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates limits
signature(object = "S2.class"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates ellipses, convex hulls and centroids
signature(object = "S2.corcircle"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and prepares the drawn grid
signature(object = "S2.density"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates densities
signature(object = "S2.distri"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates ellipses and centroids
signature(object = "S2.image"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates grid expansion and limits
signature(object = "S2.label"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default
signature(object = "S2.logo"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default
signature(object = "S2.match"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default
signature(object = "S2.traject"): calls the parent method (prepare for ADEg.S2) and modifies some graphical parameters used by default
signature(object = "S2.value"): calls the parent method (prepare for ADEg.S2), modifies some graphical parameters used by default and calculates limits
signature(object = "ADEg.T"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
signature(object = "T.image"): calls the parent method (prepare for ADEg.T) and modifies some graphical parameters used by default and calculates limits and grid
signature(object = "T.value"): calls the parent method (prepare for ADEg.T) and modifies some graphical parameters used by default and calculates limits and grid
signature(object = "ADEg.Tr"): performs the calculations before display the object (e.g. limits, grid and axis calculations)
signature(object = "Tr.class"): calls the parent method (prepare for ADEg.Tr), modifies some graphical parameters used by default and calculated ellipses, convex hulls and centroids
signature(object = "Tr.label"): calls the parent method (prepare for ADEg.Tr) and modifies some graphical parameters used by default
signature(object = "Tr.match"): calls the parent method (prepare for ADEg.Tr), modifies some graphical parameters used by default and defines the mean point and the axis
signature(object = "Tr.traject"): calls the parent method (prepare for ADEg.Tr) and modifies some graphical parameters used by default

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Mapping of a Spatial* object

Description

This function represents a background map linked with data or not.

Usage

s.Spatial(spObj, col = TRUE, nclass = 5, scale = TRUE, plot = TRUE, 
  storeData = TRUE, pos = -1, ...)

Arguments

spObj

an object deriving from class Spatial (package sp)

col

a logical or a color to fill the background color of spObj

nclass

if spObj contains data, the desired number of intervals splitting the data (using pretty)

scale

a logical indicating if numeric variables should be scaled

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.label) or ADEgS (if spObj contains more than one column ).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(elec88, package = "ade4")
## mapping without data
g1 <- s.Spatial(elec88$Spatial)

## Not run: 
  if(require(sp, quietly = TRUE)) {
    ## mapping with data
    obj <- SpatialPolygonsDataFrame(Sr = elec88$Spatial, data = elec88$tab)
    g2 <- s.Spatial(obj)
    g3 <- s.Spatial(obj, nclass = 2, col = c("red", "blue"))
  }

## End(Not run)

2-D scatter plot with arrows

Description

This function represents a two dimensional scatter plot with arrows linking points to the origin.

Usage

s.arrow(dfxy, xax = 1, yax = 2, labels = row.names(as.data.frame(dfxy)), 
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

labels

a character vector containing labels for arrows

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

An other origin for arrows can be specified using an adegpar parameters: porigin. Graphical parameters for points and arrows are available in parrows and ppoints of adegpar.

Value

An object of class ADEg (subclass S2.arrow) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(doubs, package = "ade4") 
dudi1 <- ade4::dudi.pca(doubs$env, scale = TRUE, scannf = FALSE, nf = 3)
dudi2 <- ade4::dudi.pca(doubs$fish, scale = TRUE, scannf = FALSE, nf = 2)
coin1 <- ade4::coinertia(dudi1, dudi2, scannf = FALSE, nf = 2)
g11 <- s.arrow(coin1$l1, plabels.cex = 0.87, plot = FALSE)
g12 <- s.arrow(coin1$c1, plabels.cex = 1, plabels.col = "red", plot = FALSE)
g1 <- superpose(g12, g11, plot = TRUE)

xy <- cbind(rnorm(50), rnorm(50))
g2 <- s.arrow(xy, plabels.cex = 0.9, plines = list(lwd = 1.5), parrows.angle = 20)
update(g2, plines = list(col = rainbow(5)))

2-D scatter plot with a partition in classes (levels of a factor)

Description

This function represents a two dimensional scatter plot grouping points to the same class. Classes are represented by ellipses, stars and/or convex hulls.

Usage

s.class(dfxy, fac, xax = 1, yax = 2, wt = rep(1, NROW(fac)), labels = levels(fac),
  ellipseSize = 1.5, starSize = 1, chullSize = NULL, col = NULL, facets = NULL,
  plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

fac

a factor (or a matrix of factors) splitting the rows of dfxy

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

wt

a vector of weights for fac

labels

a character vector containing the class' labels

ellipseSize

a positive number for ellipse size

starSize

a number between 0 and 1 for the size of the stars segments joining the stars' center (centroids) and the matching points

chullSize

NULL or a vector of numbers between 0 and 1 for the fraction of points included in the convex hull

col

a color or a colors vector to color points, ellipses, labels, lines and polygons

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for ellipses, stars and convex hulls are available in pellipses, plines and ppolygons of adegpar.

Value

An object of class ADEg (subclass S2.class) or ADEgS (if add is TRUE and/or if facets or multidimensional fac or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

xy <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
posi <- factor(xy$x > 0) : factor(xy$y > 0)
coul <- c("black", "red", "green", "blue")
s.class(xy, fac = posi, col = coul, psub.text = "example s.class", pellipses.col = coul)

s.class(xy, fac = posi, ppoints.cex = 1.5, ellipseSize = 0, starSize = 0,
  ppolygons = list(border = 4:1, col = 1:4, lty = 1:4, lwd = 2, alpha = 0.4),
  chullSize = c(1, 0.5))

s.class(xy, fac = posi, facets = posi, ppoints.cex = 1.5, ellipseSize = 0, starSize = 0,
  ppolygons = list(border = 4:1, col = 1:4, lty = 1:4, lwd = 2, alpha = 0.4),
  chullSize = c(1, 0.5))
  
## Not run:  
s.class(xy, fac = posi, col = coul, psub.text = "example s.class", pellipses.col = coul, 
  plabels.cex = 0, key = list(space = "left"))
   
data(banque, package = "ade4")
dudi1 <- ade4::dudi.acm(banque, scannf = FALSE)
col <- rainbow(length(levels(banque[, 20])))
g1 <- s.label(dudi1$li, psub = list(text = "Factorial map from ACM", cex = 1.5, 
  position = "topleft"), plot = FALSE)
g2 <- s.class(dudi1$li, banque[, 20], psub = list(text = names(banque)[20], cex = 1.5, 
  position = "bottomright"), ellipseSize = 0, starSize = 0.5, pgrid.text.cex = 0, plot = FALSE)
g3 <- s.class(dudi1$li, banque[, 20], starSize = 0, ellipseSize = 2, pgrid.text.cex = 0, 
  plabels.cex = 1.5, plot = FALSE)
g4 <- s.class(dudi1$li, banque[, 20], psub = list(text = names(banque)[20], 
  position = "topright"), pgrid.text.cex = 0, col = col, pellipses.lwd = 1.5, plot = FALSE)
G1 <- ADEgS(c(g1, g2, g3, g4), layout = c(2, 2))
G2 <- s.class(dudi1$li, banque, psub = list(position = "topleft"), pgrid.text.cex = 0, 
  starSize = 0, ppoints.cex = 0)

## End(Not run)

Correlation circle

Description

This function produces a correlation circle.

Usage

s.corcircle(dfxy, xax = 1, yax = 2, labels = row.names(as.data.frame(dfxy)), 
  fullcircle = TRUE, facets = NULL, plot = TRUE, storeData = TRUE, 
  add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

labels

a vector containing the points' labels

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

fullcircle

a logical to include the complete circle (limits are then c(-1, 1))

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.corcircle) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data (olympic, package = "ade4")
dudi1 <- ade4::dudi.pca(olympic$tab, scannf = FALSE)
g1 <- s.corcircle(dudi1$co)
g2 <- s.corcircle(dudi1$co, fullcircle = FALSE, pback.col = "grey")

2-D scatter plot with kernel density estimation

Description

This function represents a two dimensional scatter plot of points distribution. Densities' representation is based on the levelplot graphic in lattice (density's surface, filled with colors and/or contour lines).

Usage

s.density(dfxy, xax = 1, yax = 2, bandwidth = NULL, gridsize = c(450L, 450L), 
  nrpoints = 300, threshold = 0.1, col = NULL, contour = FALSE, region = !contour, 
  nclass = 8, facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

bandwidth

bandwidth for density calculations which is passed in parameters in the bkde2D function of the KernSmooth package

gridsize

grid dimension

nrpoints

number of points on the density image

threshold

a value between 0 and 1 to draw densities greater than this threshold. No density is visible whether it is equal to 1

col

a color or a colors vector to color densities

contour

a logical to draw contour lines

region

a logical to fill grid regions with col

nclass

number of class for density

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Density calculation is made using the kde2d function of the KernSmooth package.

Value

An object of class ADEg (subclass S2.density) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

xx2 <- c(rnorm(50000, 1, 1), rnorm(50000, -1, 1))
yy2 <- c(rnorm(50000, -1, 0.5), rnorm(50000, 1, 0.5))
s.density(cbind(xx2, yy2), paxes.draw = TRUE, gridsize = c(200, 200), region = TRUE, 
  contour = TRUE, plabels.cex = 0, threshold = 0.05, nclass = 3, 
  col = colorRampPalette(c("lightgrey", "black"))(100))

2-D scatter plot with means/standard deviations computed using an external table of weights

Description

This function represents a two dimensional scatter plot of a frequency distribution. Class are defined by ellipses and/or stars.

Usage

s.distri(dfxy, dfdistri, xax = 1, yax = 2, starSize = 1, 
  ellipseSize = 1.5, col = NULL, facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

dfdistri

a data frame containing the mass distribution in columns

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

starSize

NULL or number between 0 and 1 for the size of the stars segments joining the stars' center (centroids) and the matching points

ellipseSize

NULL or number between 0 and 1 for ellipse size

col

a color or a colors vector to color points, ellipses, labels, lines and polygons

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.distri) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(rpjdl, package = "ade4")
xy <- ade4::dudi.coa(rpjdl$fau, scan = FALSE)$li
j <- c(1, 5, 8, 20, 21, 23, 26, 33, 36, 44, 47, 49)
dfdistri <- rpjdl$fau[, j]
coli <- colorRampPalette(c("blue", "red", "orange"))(49)[j]

s.distri(xy, dfdistri, ellipseSize = 1, starSize = 0, porigin.include = FALSE, 
  pellipses = list(col = coli, alpha = 0.3), plabels.cex = 0)

2-D scatter plot with loess estimation of an additional numeric score (levelplot)

Description

This function represents a two dimensional scatter plot with a continuous convex colored surface and/or contour lines representing a third variable.

Usage

s.image(dfxy, z, xax = 1, yax = 2, span = 0.5, gridsize = c(80L, 80L), 
  contour = TRUE, region = TRUE, outsideLimits = NULL, breaks = NULL,
  nclass = 8, col = NULL, facets = NULL, 
  plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

z

a vector (or a matrix) of values on the dfxy rows

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

span

a value to control the degree of smoothing

gridsize

a 1 or 2-length vector indicating the cell numbers (horizontally and vertically) of the grid for the colored surface

contour

a logical to draw contour lines

region

a logical to fill inter-contour regions

breaks

a vector of values to split z. If NULL, pretty(z, nclass) is used.

nclass

an integer for the number of desired intervals, ignored if breaks is not missing.

outsideLimits

specific limits for the surface as a set of polygons. It must be an SpatialPolygons object. Hole are authorized.

col

a color or a colors vector used for the colored cells

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.image) or ADEgS (if add is TRUE and/or if facets or multidimensional z or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

df1 <- data.frame(expand.grid(-3:3, -3:3))
names(df1) <- c("x", "y")
z1 <- (1 / sqrt(2)) * exp(-(df1$x ^ 2 + df1$y ^ 2) / 2)
g1 <- s.image(df1, z1)

# add a continuous color bar as legend
# update(g1, plegend.drawColorKey = TRUE)

g2 <- s.image(df1, z1, gridsize = 50)

g3 <- s.image(df1, z1, gridsize = 100)
## g4 <- s.image(df1, z1, gridsize = 1000, plot = FALSE)

## Not run: 
  if(require(splancs, quietly = TRUE) & require(sp, quietly = TRUE)) {
    Sr1 <- Polygon(cbind(c(0, 1, 2, 1, 2, 0, -2, -1, -2, -1, 0), 
      c(2.5, 1.5, 2, 0, -2, -1, -2, 0, 2, 1.5, 2.5)))
    Sr2 <- Polygon(cbind(c(-0.5, 0.5, 0.5, -0.5, -0.5), c(0, 0, 1 ,1, 0)), hole = TRUE)
    Srs2 <- Polygons(list(Sr1, Sr2), ID = "star and hole")
    SPp <- SpatialPolygons(list(Srs2))
    df2 <- cbind(c(rnorm(2000, 1, 0.25), rnorm(3000, -1, 1.5)), c(rnorm(2000, 1, 0.5), 
      rnorm(3000, -1, 3)))
    z2 <- c(rnorm(2000, 12, 1), rnorm(3000, 1, 2))
    g5 <- s.image(df2, z2, outsideLimits = SPp, grid = 200, xlim = c(-2.5, 2.5), 
      ylim = c(-2, 3), ppalette.quanti = colorRampPalette(c(grey(0.1), grey(0.9))))
  
    data(t3012, package = "ade4")  
    g6 <- s.image(t3012$xy, ade4::scalewt(t3012$temp), porigin.include = FALSE)
    g7 <- s.image(t3012$xy, ade4::scalewt(t3012$temp), outsideLimits = t3012$Spatial, 
      Sp = t3012$Spatial)
  }

## End(Not run)

2-D scatter plot with labels

Description

This function represents a two dimensional scatter plot associating labels with points.

Usage

s.label(dfxy, labels = rownames(dfxy), xax = 1, yax = 2,
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, 
  pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

labels

a vector of character strings for the points' labels

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.label) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

x0 <- runif(50, -2, 2)
y0 <- runif(50, -2, 2)
z <- x0 ^ 2 + y0 ^ 2
g1 <- s.label(data.frame(x0, y0), label = as.character(z < 1), paxes.draw = TRUE, 
  axis.text = list(col = "grey"))
  
data(mafragh, package = "ade4")
g2 <- s.label(mafragh$xy, nb = mafragh$nb, paxes.draw = FALSE)

data(irishdata, package = "ade4")
g3 <- s.label(irishdata$xy.utm, Sp = irishdata$Spatial.contour)   
## update irishdata$xy.utm call to irishdata$xy

## Not run: data(atlas, package = "ade4")
  g4 <- s.label(atlas$xy, lab = atlas$names.district, Sp = atlas$Spatial.contour)
  g5 <- s.label(atlas$xy, lab = atlas$names.district, Sp = atlas$Spatial)

## End(Not run)

2-D scatter plot with logos (bitmap objects)

Description

This function represents a two dimensional scatter plot associating logos with points.

Usage

s.logo(dfxy, logos, xax = 1, yax = 2, facets = NULL, 
  plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

logos

a list containing the picture to use for each point

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.logo) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(ggtortoises, package = "ade4")
g1 <- s.logo(ggtortoises$pop, 
  ggtortoises$ico[as.character(ggtortoises$pop$carap)], 
  pori.incl = FALSE, ppoints.cex = 0.5)
g1 <- s.label(ggtortoises$pop, add = TRUE, plabels.boxes.alpha = 0)

g2 <- s.label(ggtortoises$misc, pgrid.draw = FALSE, 
  porigin.include = FALSE, paxes.draw = FALSE, 
  Sp = ggtortoises$Spatial, pback.col = "lightblue", pSp.col = "white")
g2 <- s.logo(ggtortoises$pop, ggtortoises$ico[as.character(ggtortoises$pop$carap)], 
  ppoints.cex = 0.5, add = TRUE)

data(capitales, package = "ade4")
g3 <- s.logo(capitales$xy[sort(rownames(capitales$xy)), ], capitales$logo, 
  Sp = capitales$Spatial, pback.col = "lightblue", pSp.col = "white", 
  pgrid.draw = FALSE)

2-D scatter plot of the matching between two sets of coordinates

Description

This function represents a two dimensional scatter plot linking paired coordinates.

Usage

s.match(dfxy1, dfxy2, xax = 1, yax = 2, labels =
  row.names(as.data.frame(dfxy1)), arrows = TRUE, 
  facets = NULL, plot = TRUE, storeData = TRUE, 
  add = FALSE, pos = -1, ...)

Arguments

dfxy1

a data frame, the first system of coordinates, used to produce the plot

dfxy2

a data frame, the second system of coordinates, with as many rows as dfxy1, used to produce the plot.

labels

a vector of character strings containing the matches' labels

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

arrows

a logical to draw arrows

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.match) or ADEgS (if add is TRUE and/or if facets or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

X <- data.frame(x = runif(50, -1, 2), y = runif(50, -1, 2))
Y <- X + rnorm(100, sd = 0.3)
g1 <- s.match(X, Y, arr = TRUE, ppoints.cex = 2, ppoints.col = c("blue", "green"))

data(doubs, package = "ade4")
dudi1 <- ade4::dudi.pca(doubs$env, scale = TRUE, scannf = FALSE, nf = 3)
dudi2 <- ade4::dudi.pca(doubs$fish, scale = FALSE, scannf = FALSE, nf = 2)
coin1 <- ade4::coinertia(dudi1, dudi2, scannf = FALSE, nf = 2)
g2 <- s.match(dfxy1 = coin1$mX, dfxy2 = coin1$mY)

2-D scatter plot with trajectories

Description

This function represents a two dimensional scatter plot with trajectories.

Usage

s.traject(dfxy, fac = gl(1, nrow(dfxy)), order, labels = levels(fac), 
  xax = 1, yax = 2, col = NULL, facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

fac

a factor (or a matrix of factors) splitting the rows of dfxy

order

a vector containing the drawing order of the trajectories. A vector of length equal to factor.

labels

a vector of character strings containing the trajectories' labels

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

col

a color or a colors vector to color points, labels and lines

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

The fac factor is used to display several trajectories: each level of fac is a specific trajectory.

Value

An object of class ADEg (subclass S2.traject) or ADEgS (if add is TRUE and/or if facets or multidimensional fac or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

rw <- function(a) {
  x <- 0
  for(i in 1:49) x <- c(x, x[length(x)] + runif(1, -1, 1))
  x
}
x1 <- unlist(lapply(1:5, rw), use.names = FALSE)
y1 <- unlist(lapply(1:5, rw), use.names = FALSE)
z1 <- gl(5, 50)
g1 <- s.traject(data.frame(x1, y1), z1, ppoints.pch = 19:23, plines.col = rainbow(5))

x2 <- unlist(lapply(1:2, rw), use.names = FALSE)
y2 <- unlist(lapply(1:2, rw), use.names = FALSE)
z2 <- gl(2, 50)
g2 <- s.traject(data.frame(x2, y2), z2, ppoints.pch = 21:20, plines.col = 1:2)

2-D scatter plot with proportional symbols (bubble plot)

Description

This function represents a two dimensional scatter plot with a third value represented by symbols.

Usage

s.value(dfxy, z, breaks = NULL, xax = 1, yax = 2, method = c("size",
"color"), symbol = c("square", "circle", "diamond", "uptriangle", "downtriangle"),
col = NULL, nclass = 4, center = 0, centerpar = NULL, facets = NULL,
plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxy

a data frame used to produce the plot

z

a vector (or a matrix) with as many values as rows in dfxy

breaks

a vector containing the breaks used for splitting z value. If NULL, pretty(z, n) is used.

xax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the x-axis

yax

an integer (or a vector) indicating which column(s) of dfxy is(are) plotted on the y-axis

method

color or size value for represent z. If color, a palette of color is used for the symbols (one color per interval). If size, symbols of proportional area are used. Area is 0 for values equals to center (default 0). Two colors are used, for values less than center and larger than center.

symbol

value for symbol type

col

a color or a colors vector to color symbols. If method is size, a 2-length vector of color is expected. If method is color, it must have as many colors as the number of class.

nclass

an integer for the number of desired intervals, ignored if breaks is not missing.

center

a center value for method size

centerpar

a logical or a list to represent center value using elements in the adegpar("ppoints") list

facets

a factor splitting the rows of dfxy so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass S2.value) or ADEgS (if add is TRUE and/or if facets or multidimensional z or vectors for xax/yax are used).
The result is displayed if plot is TRUE.

Note

For the symbol size, if the method is size, we use perceptual scaling (Tanimura et al. 2006) .

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Tanimura, S. and Kuroiwa, C. and Mizota, T. 2006 Proportional symbol mapping in R Journal of Statistical Software 15, 1–7

Examples

 
data(rpjdl, package = "ade4")
fau.coa <- ade4::dudi.coa(rpjdl$fau, scan = FALSE, nf = 3)
g1 <- s.value(fau.coa$li, fau.coa$li[,3])
update(g1, key = list(space = "right", columns = 1))
g2 <- s.value(fau.coa$li, fau.coa$li[,3], method = "color", plegend.size = 0.8)
g3 <- s.value(fau.coa$li, fau.coa$li[,3], plegend.size = 0.8, symbol = "square",
   method = "color",  col = colorRampPalette(c("yellow", "blue"))(6))
g4 <- s.value(fau.coa$li, fau.coa$li[,3], plot = FALSE)
g5 <- s.value(fau.coa$li, fau.coa$li[, 3], center = 0, method = "size", 
  symbol = "circle", col = c("yellow", "red"), plot = FALSE)
g6 <- ADEgS(c(g4, g5), positions = layout2position(matrix(c(1, 2), 1, 2)), 
  add = matrix(0, ncol = 2, nrow = 2))  
   
data(irishdata, package = "ade4")
irq0 <- data.frame(scale(irishdata$tab, scale = TRUE))
g7 <- s.value(irishdata$xy.utm, irq0, Sp = irishdata$Spatial.contour, paxes.draw = FALSE, 
  pgrid.draw = FALSE, pSp.alpha = 0.4)

1-D plot of a numeric score by bars

Description

This function represents a score using a chart with rectangular bars for which length is proportional to this score.

Usage

s1d.barchart(score, labels = NULL, at = 1:NROW(score), sort = FALSE,
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

labels

the labels' names drawn on the top of bars

at

a numeric vector used as an index

sort

a logical indicating if score is sorted in ascending order

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for bars are available in ppolygons of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.barchart) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(rpjdl, package = "ade4")
rpjdl.coa <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
s1d.barchart(rpjdl.coa$eig, p1d.horizontal = FALSE, ppolygons.col = "grey")

1-D box plot of a numeric score partitioned in classes (levels of a factor)

Description

This function represents the link between a variable and a set of qualitative variables using box-and-whisker plots.

Usage

s1d.boxplot(score, fac = gl(1, NROW(score)), at = 1:nlevels(fac), col = NULL, 
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

fac

a factor (or a matrix of factors) to split score

at

a numeric vector used as an index

col

a color or a colors vector for points, labels, lines and polygons according to their factor level. Colors are recycled whether there are not one color by factor level.

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for rugs are available in plines of adegpar and the ones for boxes in ppolygons. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass S1.boxplot) or ADEgS (if add is TRUE and/or if facets or data frame for score or data frame for fac are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(banque, package = "ade4")
banque.acm <- ade4::dudi.acm(banque, scan = FALSE, nf = 4)
s1d.boxplot(banque.acm$l1[, 1], banque[, 2], psub.text = names(banque)[2], 
  psub.position = "topleft", col = c("red", "blue", "green", "purple", "orange"))
s1d.boxplot(banque.acm$l1[,1], banque[, 1:6], psub.position = "topleft")

1-D plot of a numeric score partitioned in classes (levels of a factor)

Description

This function represents the link between scores values and their matching labeled classes.

Usage

s1d.class(score, fac, wt = rep(1, NROW(fac)), labels = levels(fac), at = 0.5, 
  poslabel = c("regular", "value"), col = NULL, facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

fac

a factor (or a matrix of factors) to split score

wt

a vector of weights for score

labels

the labels' names drawn for each class

at

a numeric vector used as an index

poslabel

the label position of each class (each level of fac), it can be regular or value. If regular, labels are evenly spaced. If value, labels are placed on the weighted mean of their class.

col

a color or a colors vector for points, labels and lines according to their factor level. Colors are recycled whether there are not one color by factor level.

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

The weighted means of class are available in the object slot stats using object@stats$means. Graphical parameters for rugs are available in plines of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass S1.class) or ADEgS (if add is TRUE and/or if facets or data frame for score or data frame for fac are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(meau, package = "ade4")
envpca <- ade4::dudi.pca(meau$env, scannf = FALSE)

g1 <- s1d.class(envpca$li[, 1], meau$design$season, poslabel = "value", col = 1:4, plot = FALSE)
g2 <- s1d.class(envpca$li[, 1], meau$design$season, poslabel = "regular", col = 1:6, 
  p1d.reverse = TRUE, plot = FALSE)
ADEgS(c(g1, g2), layout = c(2, 1))

g3 <- s1d.class(envpca$li[, 1], meau$design$season, poslabel = "value", col = 1:4, 
  plabels.cex = 0, key = list(space = "bottom"))

1-D plot of a numeric score linked by curves

Description

This function represents a score using points linked by curves.

Usage

s1d.curve(score, at = 1:NROW(score), facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

at

a numeric vector used as an index

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for lines and points are available in plines and in ppoints of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.curve) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(rpjdl, package = "ade4")
rpjdl.coa <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
s1d.curve(rpjdl.coa$eig)

set.seed(40)
score1 <- rnorm(10)
s1d.curve(score1)

1-D plot of multiple scores linked by curves

Description

This function represents multiple scores using points linked by curves.

Usage

s1d.curves(score, at = 1:NROW(score), facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric matrix (or a data frame) used to produce the plot

at

a numeric vector used as an index

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for lines and points are available in plines and in ppoints of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.curves) or ADEgS (if add is TRUE and/or if facets are used).
The result is displayed if plot is TRUE.

Author(s)

Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples


scores <- matrix(1:50, nrow = 10)
s1d.curves(scores)

1-D plot of a numeric score by density curves

Description

This function represents a score with a density curve for each level of a factor.

Usage

s1d.density(score, fac = gl(1, NROW(score)), kernel = c("normal", "box", 
  "epanech", "biweight", "triweight"), bandwidth = NULL, gridsize = 450, 
  col = NULL, fill = TRUE, facets = NULL, plot = TRUE, storeData = TRUE,
  add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

fac

a factor (or a matrix of factors) to split score

kernel

the smoothing kernel used, see bkde

bandwidth

the kernel bandwidth smoothing parameter

gridsize

the number of equally spaced points at which to estimate the density

col

a logical, a color or a colors vector for labels, rugs, lines and polygons according to their factor level. Colors are recycled whether there are not one color by factor level.

fill

a logical to yield the polygons density curves filled

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

kernel, bandwidth and gridsize are passed as parameters to bkde function of the KernSmooth package.

Graphical parameters for rugs are available in plines of adegpar and the ones for density curves filled in ppolygons. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.density) or ADEgS (if add is TRUE and/or if facets or data frame for score or data frame for fac are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

score <- c(rnorm(1000, mean = -0.5, sd = 0.5), rnorm(1000, mean = 1))
fac <- rep(c("A", "B"), each = 1000)
s1d.density(score, fac, col = c(2, 4), p1d.reverse = TRUE)

1-D plot of a numeric score by means/standard deviations computed using an external table of weights

Description

This function represents a set of distributions on a numeric score using a mean-standard deviation display

Usage

s1d.distri(score, dfdistri, labels = colnames(dfdistri), at = 1:NCOL(dfdistri), 
  yrank = TRUE, sdSize = 1, facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

dfdistri

a data frame containing the mass distribution in which each column is a class

yrank

a logical to draw the distributions sorted by means ascending order

labels

the labels' names drawn for each distribution

at

a numeric vector used as an index

sdSize

a numeric for the size of the standard deviation segments

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for rugs are available in plines of adegpar. Some appropriated graphical parameters in p1d are also available. The weighted means and standard deviations of class are available in the object slot stats using object@stats$means and object@stats$sds.

Value

An object of class ADEg (subclass S1.distri) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

w <- seq(-1, 1, le = 200)
distri <- data.frame(lapply(1:50, 
  function(x) sample(200:1) * ((w >= (- x / 50)) & (w <= x / 50))))
names(distri) <- paste("w", 1:50, sep = "")
g11 <- s1d.distri(w, distri, yrank = TRUE, sdS = 1.5, plot = FALSE)
g12 <- s1d.distri(w, distri, yrank = FALSE, sdS = 1.5, plot = FALSE)
G1 <- ADEgS(c(g11, g12), layout = c(1, 2))

data(rpjdl, package = "ade4")
coa1 <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE)
G2 <- s1d.distri(coa1$li[,1], rpjdl$fau, labels = rpjdl$frlab, 
  plabels = list(cex = 0.8, boxes = list(draw = FALSE)))

## Not run: 
g31 <- s1d.distri(coa1$l1[,1], rpjdl$fau, plabels = list(cex = 0.8, boxes = list(draw = FALSE)), 
  plot = FALSE)
nsc1 <- ade4::dudi.nsc(rpjdl$fau, scannf = FALSE)
g32 <- s1d.distri(nsc1$l1[,1], rpjdl$fau, plabels = list(cex = 0.8, boxes = list(draw = FALSE)), 
  plot = FALSE)
g33 <- s.label(coa1$l1, plot = FALSE)
g34 <- s.label(nsc1$l1, plot = FALSE)
G3 <- ADEgS(c(g31, g32, g33, g34), layout = c(2, 2))

## End(Not run)

1-D plot of a numeric score by dots

Description

This function represents a score using dots.

Usage

s1d.dotplot(score, at = 1:NROW(score), facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

at

a numeric vector used as an index

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for segments and dots are available in plines and in ppoints of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.dotplot) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(rpjdl, package = "ade4")
rpjdl.coa <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
s1d.dotplot(rpjdl.coa$eig)

set.seed(40)
score1 <- rnorm(10)
s1d.dotplot(score1)

1-D plot of a numeric score by Gaussian curves

Description

This function represents a score with a Gauss curve for each level of a factor.

Usage

s1d.gauss(score, fac = gl(1, NROW(score)), wt = rep(1,
  NROW(score)), steps = 200, col = NULL, fill = TRUE,
  facets = NULL, plot = TRUE, storeData = TRUE, add =
  FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

fac

a factor (or a matrix of factors) to split score

wt

a vector of weights for score

steps

a value for the number of segments used to draw the Gauss curves

col

a logical, a color or a colors vector for labels, rugs, lines and polygons according to their factor level. Colors are recycled whether there are not one color by factor level.

fill

a logical to yield the polygons Gauss curves filled

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for rugs are available in plines of adegpar and the ones for Gauss curves filled in ppolygons. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.gauss) or ADEgS (if add is TRUE and/or if facets or data frame for score or data frame for fac are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(meau, package= "ade4")
envpca <- ade4::dudi.pca(meau$env, scannf = FALSE)
dffac <- cbind.data.frame(meau$design$season, meau$design$site)
g1 <- s1d.gauss(envpca$li[, 1], fac = dffac, fill = TRUE, col = 1:6)
update(g1, steps = 10)
g2 <- s1d.gauss(envpca$li[, 1], dffac[, 2], ppoly.col = 1:4, paxes.draw = TRUE, ylim = c(0, 2), 
  fill = TRUE, p1d.hori = FALSE)

1-D plot of a numeric score by bars

Description

This function represents a score using a chart with rectangular bars.

Usage

s1d.hist(score, breaks = NULL, nclass = round(log2(length(score)) + 1), 
  type = c("count", "density", "percent"), right = TRUE, facets = NULL, 
  plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

breaks

a vector of values to split score. If NULL, pretty(score, nclass) is used.

nclass

an integer for the number of desired intervals, ignored if breaks is not missing.

type

a value among count, density, percent to indicate the unit of the cell height.

right

a logical indicating if the histogram cells are right-closed (left open) intervals.

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for polygons are available in ppolygons of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.hist) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

set.seed(40)
score1 <- rnorm(1000)
s1d.hist(score1)

1-D plot of the interval between two numeric scores

Description

This function represents the interval between two scores using either segments or filled areas.

Usage

s1d.interval(score1, score2, at = 1:NROW(score1), method = c("bars", "area"), 
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

score1

a numeric vector (or a data frame) used to produce the plot

score2

a numeric vector with as many values as values (or rows) in score1

at

a numeric vector used as an index

method

a value, bars or area, to represent either segments or areasbetween scores.

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for polygons, lines and segment boundaries are available in respectively ppolygons, plines and parrows of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass C1.interval) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

set.seed(40)
sc1 <- rnorm(10)
sc2 <- rnorm(10)
s1d.interval(sc1, sc2, method = "bars")
s1d.interval(sc1, sc2, method = "area")

1-D plot of a numeric score with labels

Description

This function represents a numeric labeled score

Usage

s1d.label(score, labels = 1:NROW(score), at = 0.5, poslabel = c("regular",
  "value"), facets = NULL, plot = TRUE, storeData =
  TRUE, add = FALSE, pos = -1, ...)

Arguments

score

a numeric vector (or a data frame) used to produce the plot

labels

the labels' names drawn for each score value

at

a numeric vector used as an index

poslabel

the label position, it can be regular or value. If regular, labels are evenly spaced. If value, labels are placed on the weighted mean of their class.

facets

a factor splitting score so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for rugs are available in plines of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass S1.label) or ADEgS (if add is TRUE and/or if facets or data frame for score are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(meau, package = "ade4")
envpca <- ade4::dudi.pca(meau$env, scannf = FALSE)
g1 <- s1d.label(envpca$l1[, 1], row.names(envpca$l1), plot = FALSE)
g2 <- s1d.label(envpca$co[, 1], row.names(envpca$co), p1d.reverse = TRUE, plot = FALSE)
G <- ADEgS(c(g1, g2), layout = c(2, 1))

1-D plot of the matching between two numeric scores

Description

This function represents paired scores with evenly spaced labels.

Usage

s1d.match(score1, score2, labels = 1:NROW(score1), at = 0.5, 
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, 
  pos = -1, ...)

Arguments

score1

a numeric vector (or a data frame) used to produce the plot

score2

a numeric vector used to produce the plot with as many values as values (or rows) in score1

labels

the labels' names drawn for each score1 value

at

a numeric vector used as an index

facets

a factor splitting score1 so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

Graphical parameters for rugs are available in plines of adegpar. Some appropriated graphical parameters in p1d are also available.

Value

An object of class ADEg (subclass S1.match) or ADEgS (if add is TRUE and/or if facets or data frame for score or data frame for fac are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

s1d.match(-5:5, 2 * (-5:5))

Computes limits for 1D and 2D displays.

Description

Computes limits for 1D and 2D displays adding 10% of margins around the extreme values.

Usage

setlimits1D(mini, maxi, origin, includeOr)
setlimits2D(minX, maxX, minY, maxY, origin = c(0, 0), aspect.ratio = "iso", includeOr)

Arguments

mini

the smallest value of a unidimensional dataset

maxi

the largest value of a unidimensional dataset

minX

the smallest value of the first dimension of a bidimensional dataset

maxX

the largest value of the first dimension of a bidimensional dataset

minY

the smallest value of the second dimension of a bidimensional dataset

maxY

the largest value of the second dimension of a bidimensional dataset

origin

a value (in setlimits1D) or a two-length vector (in setlimits2D) indicating origin coordinate(s)

aspect.ratio

a character string to control physical aspect ratio of the graphic. iso for isometric scales, fill for drawing as big as possible or xy for banking rule

includeOr

a boolean value indicating whether the origin is included in the graphics window

Value

setlimits1D returns a two-length vector containing the limits of the graphics window on one axis.
setlimits2D returns a two-length list where the first element, named xlim, contains a two-length vector containing the limits of the graphics window on the first axis and the second, named ylim, contains the limits on the second axis.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

setlimits1D(mini = -2, maxi = 2, origin = 0, includeOr = TRUE)
setlimits2D(minX = -2, maxX = 2, minY = -3, maxY = 4, origin = c(0, 0), includeOr = TRUE)

Sort a sequence of graphical parameters

Description

Sort a sequence of graphical parameters in several lists.

Usage

sortparamADEg(...)
sortparamADEgS(..., graphsnames, nbsubgraphs = rep(1, length(graphsnames)))

Arguments

...

a sequence of graphical parameters

graphsnames

a sequence containing the name of each simple graph of the ADEgS

nbsubgraphs

a sequence containing the number of sub-graphs in each graph named in graphsnames

Value

sortparamADEg return a list of four lists named adepar, trellis, g.args and rest. sortparamADEgS return a list of as many lists as the length of graphsnames, i.e., as the number of sub-graphs of the ADEgS. The names of the lists are graphsnames and each sub-list is the result of the sortparamADEg function aplly on each sub-graph.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples


l1 <- sortparamADEg(xlab = "x-axis label", ylab = "y-axis label", plabels.cex = 1.5, 
  porigin.include = FALSE)
length(l1)
names(l1)
  
l2 <- sortparamADEgS(xlab = "x-axis label", eig.main = "Eigenvalues", row.ppoints.col = "red",
  porigin.include = FALSE, graphsnames = c("row", "col", "eig"))
names(l2)
names(l2$row)

l3 <- sortparamADEgS(xlab = "x-axis label", eig.main = "Eigenvalues", row.ppoints.col = "pink",
  porigin.include = FALSE, graphsnames = c("row", "col", "eig"), nbsubgraphs = c(1, 2, 1))
names(l3)
length(l3$row)
length(l3$col)

Superpose two graphics

Description

This function superposes two graphics and extends the graphical constraints of a first graphic to a second one.

Usage

superpose(g1, g2, which, plot = FALSE)
## S4 method for signature 'ADEg'
e1 + e2

Arguments

g1

an object of class ADEg, ADEgS or trellis

g2

an object of class ADEg, ADEgS or trellis superposed on g1

e1

an object of class ADEg or ADEgS

e2

an object of class ADEg or ADEgS superposed on e1

which

if g1 is an ADEgS, which ADEg is used as the base of superposition (g2 is superposed on g1[[which]])

plot

a logical indicating if the graphics is displayed

Details

The created ADEgS object is a layout of two graphical objects. Each of the two objects superposed still have its graphical parameters in the created layout. However, the ADEgS displayed favour the graphical parameters of the object below : displayed limits, grid, legend and axes are those of g1 (respectively e1) and g2 (respectively e2) has transparent background and labels' boxes.

The superpose method is defined for:

signature(g1 = "ADEgS", g2 = "ADEg", which = "numeric", plot = "logical")
signature(g1 = "ADEgS", g2 = "ADEg", which = "numeric", plot = "ANY")
signature(g1 = "ADEgS", g2 = "ADEg", which = "missing", plot = "ANY"): If which is missing, the last ADEg of g1@ADEglist is used as the base of superposition. In that case, which = length(g1)
signature(g1 = "ADEgORtrellis", g2 = "ADEgORtrellis", which = "ANY", plot = "ANY"): If g1 is an ADEg object, no which is needed.
signature(g1 = "ADEgS", g2 = "ADEgS", which = "missing", plot = "ANY")

The + method is defined for:

signature(e1 = "ADEg", e2 = "ADEg"): superpose e2 on e1
signature(e1 = "ADEg", e2 = "ADEgS"): superpose e2 to e1
signature(e1 = "ADEgS", e2 = "ADEg"): calls the + method with signature (e1 = "ADEg", e2 = "ADEgS").

Value

An object of class "ADEgS".

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

cha <- LETTERS[1:20]
xy <- cbind.data.frame(runif(length(cha)), runif(length(cha)))
g1 <- s.label(xy, labels = cha, ppoints.alpha = 0, pbackground.col = "grey85")
g2 <- s.label(xy, labels = cha, plabels.cex = 0, paxes.draw = TRUE, ppoints.pch = 4, 
  ppoints.col = "red")
g3 <- superpose(g1, g2, plot = TRUE)
g4 <- superpose(g2, g1, plot = TRUE)

data(jv73, package = "ade4")
pca1 <- ade4::dudi.pca(jv73$morpho, scannf = FALSE)
g5 <- s.label(pca1$li, plabels.optim = TRUE)
g6 <- s.class(pca1$li, jv73$fac.riv, starSize = 0, ellipseSize = 0, chullSize = 1, 
  ppolygons.alpha = 0.4, col = rainbow(12), ppoints.cex = 0)
g5 + g6

## Not run: g7 <- s.label(pca1$li, plabels.optim = TRUE, facets = jv73$fac.riv, plot = FALSE)
g8 <- s.class(pca1$li, jv73$fac.riv, facets = jv73$fac.riv, starSize = 0, chullSize = 1, 
  ellipseSize = 0, ppolygons.alpha = 0.4, col = rainbow(12), ppoints.cex = 0, plot = FALSE)
g9 <- superpose(g7, g8, plot = TRUE)

## End(Not run)

Heat map-like representation with colored cells

Description

This function represents a two dimensional table plot in which cells are colored according with their value.

Usage

table.image(dftab, coordsx = 1:ncol(as.matrix(dftab)), coordsy =
  nrow(as.matrix(dftab)):1, labelsx, labelsy, nclass = 3,
  breaks = NULL, col = NULL, plot = TRUE, storeData =
  TRUE, add = FALSE, pos = -1, ...)

Arguments

dftab

a data frame, matrix, contingency table or distance matrix used to produce the plot

coordsx

an integer or a vector indicating the columns of dftab kept

coordsy

an integer or a vector indicating the rows of dftab kept

labelsx

columns labels

labelsy

rows labels

breaks

a vector of values to split dftab. If NULL, pretty(dftab, nclass) is used.

nclass

an integer for the number of desired intervals, ignored if breaks is not missing.

col

a color or a colors vector used for the cells

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass T.image) or ADEgS (if add is TRUE).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

tab <- as.table(matrix(rnorm(900), ncol = 30))
g1 <- table.image(tab)

# add a continuous color bar as legend
# update(g1, plegend.drawColorKey = TRUE)

g2 <- table.image(tab, n = 100, coordsx = c(30, 1:29), plegend.drawKey = FALSE)

data(rpjdl, package = "ade4")
X <- data.frame(t(rpjdl$fau))
Y <- data.frame(t(rpjdl$mil))
coa1 <- ade4::dudi.coa(X, scannf = FALSE)
g3 <- table.image(Y, coordsx = rank(coa1$co[, 1]), coordsy = 1:8, nclas = 5, 
  labelsx = "", plegend.drawKey = FALSE)

Heat map-like representation with proportional symbols

Description

This function represents a two dimensional table plot with proportional or colored squares or circles for each value.

Usage

table.value(dftab, coordsx = 1:ncol(as.matrix(dftab)), coordsy =
nrow(as.matrix(dftab)):1, labelsx, labelsy, breaks = NULL, method =
c("size", "color"), symbol = c("square", "circle", "diamond",
"uptriangle", "downtriangle"), col = NULL, nclass = 3, center = 0,
centerpar = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dftab

a data frame, matrix, contingency table or distance matrix used to produce the plot

coordsx

an integer or a vector indicating the columns of dftab kept

coordsy

an integer or a vector indicating the rows of dftab kept

labelsx

columns labels

labelsy

rows labels

breaks

a vector of values to split dftab. If NULL, pretty(dftab, nclass) is used.

method

symbol

value for symbol type

col

a color or a colors vector to color symbols. If method is size, a 2-length vector of color is expected. If method is color, it must have as many colors as the number of class

nclass

an integer for the number of desired intervals, ignored if breaks is not missing.

center

a center value for method size

centerpar

a logical or a list to represent center value using elements in the adegpar("ppoints") list

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data should be stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass T.cont if dftab is an table object, otherwise subclass T.value) or ADEgS (if add is TRUE).
The result is displayed if plot is TRUE.

Note

For the symbol size, if the method is size, we use perceptual scaling (Tanimura et al. 2006) .

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

References

Tanimura, S. and Kuroiwa, C. and Mizota, T. 2006 Proportional symbol mapping in R Journal of Statistical Software 15, 1–7

Examples

## data.frame
data(olympic, package = "ade4")
w <- olympic$tab
w <- data.frame(scale(w))
wpca <- ade4::dudi.pca(w, scann = FALSE)
g1 <- table.value(w, ppoints.cex = 0.5, axis.line = list(col = "darkblue"), 
  axis.text = list(col = "darkgrey"))
  
# update the legend position
update(g1, key = list(space = "left"))
update(g1, key = list(columns = 1))

g2 <- table.value(w, coordsy = rank(wpca$li[, 1]), ppoints.cex = 0.5, 
  axis.line = list(col = "darkblue"), axis.text = list(col = "darkgrey"))
g3 <- table.value(w, coordsy = wpca$li[, 1], coordsx = wpca$co[, 1], ppoints.cex = 0.5, 
  axis.line = list(col = "darkblue"), axis.text = list(col = "darkgrey"))

## distance
data(eurodist)
g5 <- table.value(eurodist, symbol = "circle", 
  ptable.margin = list(bottom = 5, top = 16, left = 5, right = 16))

## Not run: 
## table
data(rpjdl, package = "ade4")
w <- data.frame(t(rpjdl$fau))
wcoa <- ade4::dudi.coa(w, scann = FALSE)
g6 <- table.value(as.table(as.matrix(w)), meanY = TRUE, coordsx = wcoa$c1[,1], 
  coordsy = rank(wcoa$l1[,1]), ppoints.cex = 0.2, labelsx = "", col = "black")

## End(Not run)

Ternary plot with a partition in classes (levels of a factor)

Description

This function represents a three dimensional scatter plot with a partition in classes (levels of a factor).

Usage

triangle.class(dfxyz, fac, wt = rep(1, NROW(fac)), labels = levels(fac), 
  col = NULL, ellipseSize = 1, starSize = 1, chullSize = NULL, adjust = TRUE, 
  min3d = NULL, max3d = NULL, showposition = TRUE, facets = NULL, plot = TRUE, 
  storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxyz

a three columns data frame used to produce the plot

fac

a factor (or a matrix of factors) splitting the rows of dfxyz

wt

a vector of weights for fac

labels

a character vector containing the class' labels

col

a logical, a color or a colors vector to color points, ellipses, labels, lines and polygons

ellipseSize

a positive number for ellipse size

starSize

a number between 0 and 1 for the size of the stars segments joining the stars' center (centroids) and the matching points

chullSize

NULL or a vector of numbers between 0 and 1 for the fraction of points included in the convex hull

adjust

a logical to adjust the device with the limits of the smaller equilateral triangle containing the values

min3d

a vector of three values for triangular minimal limits

max3d

a vector of three values for triangular maximal limits

showposition

a logical indicating whether the used triangle should be shown in the complete one

facets

a factor splitting the rows of dfxyz so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass Tr.class) or ADEgS (if showposition is TRUE, if add is TRUE and/or if facets are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(euro123, package = "ade4")
fac1 <- euro123$plan$an
df1 <- rbind.data.frame(euro123$in78, euro123$in86, euro123$in97)
triangle.class(df1, fac = fac1, showposition = TRUE, col = c(1, 2, 3))
triangle.class(df1, fac = fac1, showposition = FALSE, plabels.cex = 0, col = c(1, 2, 3), 
  key = list(space = "left"))

Ternary plot with labels

Description

This function represents a three dimensional scatter plot with labels.

Usage

triangle.label(dfxyz, labels = rownames(dfxyz), adjust = TRUE, min3d = NULL, 
  max3d = NULL, addaxes = FALSE, addmean = FALSE, meanpar = NULL, axespar = NULL, 
  showposition = TRUE, facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, 
  pos = -1, ...)

Arguments

dfxyz

a three columns data frame used to produce the plot

labels

a character vector containing labels for points

adjust

a logical to adjust the device with the limits of the smaller equilateral triangle containing the values

min3d

a vector of three values for triangular minimal limits

max3d

a vector of three values for triangular maximal limits

addaxes

a logical to draw the principal axes

addmean

a logical to plot the mean

meanpar

a list to represent mean points using pch, cex and col

axespar

a list to represent axes lines using col, lwd and lty

showposition

a logical indicating whether the used triangle should be shown in the complete one

facets

a factor splitting the rows of dfxyz so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass Tr.label) or ADEgS (if showposition is TRUE, if add is TRUE and/or if facets are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(euro123, package = "ade4")
df <- rbind.data.frame(euro123$in78, euro123$in86, euro123$in97)
row.names(df) <- paste(row.names(euro123$in78), rep(c(1, 2, 3), rep(12, 3)), sep = "")
g1 <- triangle.label(df, label = row.names(df), showposition = TRUE, plot = FALSE)
g2 <- triangle.label(euro123$in78, plabels.cex = 0, ppoints.cex = 2, addmean = TRUE, 
  show = FALSE, plot = FALSE)
g3 <- triangle.label(euro123$in86, labels = row.names(euro123$in78), plabels.cex = 0.8, 
  plot = FALSE)
g4 <- triangle.label(rbind.data.frame(euro123$in78, euro123$in86), plabels.cex = 0.8, 
  addaxes = TRUE, psub.te = "Principal axis", psub.cex = 1.5, psub.pos = "topright", plot = FALSE)
G <- ADEgS(c(g1, g2, g3, g4), layout = c(2, 2))

Ternary plot of the matching between two sets of coordinates

Description

This function represents a three dimensional scatter plot of paired coordinates.

Usage

triangle.match(dfxyz1, dfxyz2, labels = row.names(as.data.frame(dfxyz1)), 
  min3d = NULL, max3d = NULL, adjust = TRUE, showposition = TRUE, facets = NULL, 
  plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxyz1

a three columns data frame, the first system of coordinates, used to produce the plot

dfxyz2

a three columns data frame, the second system of coordinates, with as many rows as dfxyz1, used to produce the plot.

labels

a vector of character strings containing the matches' labels

adjust

a logical to adjust the device with the limits of the smaller equilateral triangle containing the values

min3d

a vector of three values for triangular minimal limits

max3d

a vector of three values for triangular maximal limits

showposition

a logical indicating whether the used triangle should be shown in the complete one

facets

a factor splitting the rows of dfxyz so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Value

An object of class ADEg (subclass Tr.match) or ADEgS (if showposition is TRUE, if add is TRUE and/or if facets are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(euro123, package = "ade4")
triangle.match(euro123$in78, euro123$in86, plabels.cex = 0.8)

Ternary plot with trajectories

Description

This function represents a three dimensional scatter plot with trajectories.

Usage

triangle.traject(dfxyz, fac = gl(1, nrow(dfxyz)), order, labels = levels(fac), 
  col = NULL, adjust = TRUE, min3d = NULL, max3d = NULL, showposition = TRUE, 
  facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...)

Arguments

dfxyz

a three columns data frame, the first system of coordinates, used to produce the plot

fac

a factor (or a matrix of factors) splitting the rows of dfxyz

order

a vector containing the drawing order of the trajectories. A vector of length equal to factor.

labels

a vector of character strings containing the trajectories' labels

col

a color or a colors vector to color points, labels and lines

adjust

a logical to adjust the device with the limits of the smaller equilateral triangle containing the values

min3d

a vector of three values for triangular minimal limits

max3d

a vector of three values for triangular maximal limits

showposition

a logical indicating whether the used triangle should be shown in the complete one

facets

a factor splitting the rows of dfxyz so that subsets of the data are represented on different sub-graphics

plot

a logical indicating if the graphics is displayed

storeData

a logical indicating if the data are stored in the returned object. If FALSE, only the names of the data arguments are stored

add

a logical. If TRUE, the graphic is superposed to the graphics already plotted in the current device

pos

an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if storeData is FALSE

...

additional graphical parameters (see adegpar and trellis.par.get)

Details

The fac factor is used to display several trajectories: each level of fac is a specific trajectory.

Value

An object of class ADEg (subclass Tr.traject) or ADEgS (if showposition is TRUE, if add is TRUE and/or if facets are used).
The result is displayed if plot is TRUE.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

exo1 <- matrix(c(51.88, 32.55, 15.57, 44.94, 34.59, 20.47, 25.95, 39.15, 34.9,
  37.87, 43.19, 18.94, 34.2, 43.32, 22.48, 16.13, 42.18, 41.69,
  7.76, 70.93, 21.31, 6.22, 65.96, 27.82, 6.44, 57.06, 36.5,
  37.24, 32.45, 30.31, 16.09, 31.22, 52.69, 6.54, 24.68, 68.78), 
  ncol = 3, byr = TRUE)
exo1 <- as.data.frame(exo1)
names(exo1) <- c("agr", "ouv", "ter")
com <- as.factor(rep(c("Gig", "Lun", "Gan", "Mat"), c(3, 3, 3, 3)))
rec <- as.factor(rep(c("68", "75", "82"), 4))
row.names(exo1) <- paste(com, rec, sep = "")
tri1 <- triangle.traject(exo1, fac = com, showposition=FALSE, 
 pgrid.draw = FALSE, col = TRUE, axis.text = list(cex = 0))

Zoom in or out

Description

This function performs a zoom on a ADEg.S1 or ADEg.S2 displayed object.

Usage

zoom(object, zoom, center)

Arguments

object

a ADEg.S1 or ADEg.S2 object

zoom

a numeric value to zoom in (if zoom > 1) or out (if zoom < 1)

center

a numeric value (if object is a ADEg.S1 object) or a two-length vector (if object is a ADEg.S2 object) as a reference point to zoom (in or out). If it is missing, the displayed center point is used.

Value

Updated display after zoom.

Author(s)

Alice Julien-Laferriere, Aurelie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Stephane Dray

Examples

data(olympic, package = "ade4")
dudi1 <- ade4::dudi.pca(olympic$tab, scan = FALSE)
g <- s.corcircle(dudi1$co, lab = names(olympic$tab), fullcircle = TRUE, psub.text = "data:olympic")
zoom(g, 0.5)
zoom(g, 2, center = c(-0.4, 0.8))

Graphical objects for ade4 functions (and more)

Description

Details

References

See Also

Examples

Class ADEg

Description

Objects from the Class

Slots

Methods

Note

Author(s)

See Also

Examples

Class ADEg.C1

Description

Objects from the Class

Slots

Extends

Methods

Note

Author(s)

See Also

Examples

Class ADEg.S1

Description

Objects from the Class

Slots

Extends

Methods

Note

Author(s)

See Also

Examples

Class ADEg.S2

Description

Objects from the Class

Slots

Extends

Methods

Author(s)

See Also

Examples

Class ADEg.T

Description

Objects from the Class

Slots

Extends

Methods

Author(s)

See Also

Examples

Class "ADEg.Tr"

Description

Objects from the Class

Slots

Extends

Methods

Author(s)

See Also

Examples

Creation of ADEgS objects

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Class "ADEgS"

Description

Objects from the Class

Slots

Methods

Author(s)

See Also

Examples

Class C1.barchart

Description

Class `ADEg`

Class `ADEg.C1`

Class `ADEg.S1`

Class `ADEg.S2`

Class `ADEg.T`

Class `"ADEg.Tr"`

Creation of `ADEgS` objects

Class `"ADEgS"`

Class `C1.barchart`

Class `C1.curve`

Class `C1.density`

Class `C1.dotplot`

Class `C1.gauss`

Class `C1.hist`

Class `C1.interval`

Class `S1.boxplot`