An R package to visualise data on a Lifemap base (https://lifemap-ncbi.univ-lyon1.fr/)
To install the development version of LifemapR
from
GitHub :
::install_github("damiendevienne/LifemapR") remotes
Once installed, load the package with :
require("LifemapR")
Here is a brief introduction on how to use LifemapR.
build_Lifemap
function transform your already
existing data into a format usable by LifemapR functionsdata(eukaryotes_1000)
# Construction of a LifemapR usable dataframe
<- LifemapR::build_Lifemap(eukaryotes_1000) LM_obj
After the build_Lifemap
function the result is a
LifemapR format containing a dataframe :
<- LM_obj$df full_df
LifemapR
functions. Note that with the
LifemapR
functions, a shiny
application will
be launched# Initialise a visualisation for LM_obj
lifemap(LM_obj) +
# adding a subtree with colored branches
::lm_branches(var_col = "Protein", FUN = mean, col = "PiYG")+
LifemapR# adding a set of points
::lm_markers(radius = "GC.", var_fillColor = "Genes", FUN = mean) LifemapR
To do list :
New protocole to fetch data with improved databases (parquet format)
Improve create_matrix() to use less CPU (merge before joining all lists)
Improve make_newick() to make it recursive
Improve the shiny application version
Redo pass_info function to only infer unknown values and only from the value of direct ancestors
Implement popups and labels for markers
Implement popups and labels for polylines
Black background on leaflet
Repair the size legend
Option to thicker the line depending on a variable
Improve create_matrix function to pass check
Go to the package’s folder
require(devtools)
::load_all() devtools
then you can simply use the package’s functions