object name.

output file from Cell Ranger used for creation of Seurat object. (Either provide this of hdf5_file)

output file from Cell Ranger used for creation of Seurat object. (Either provide this of features_tsv_file)

name of assay(s) to add the alternative features to. Can specify "all" to add to all assays.

name to use for data.frame when stored in ⁠@misc⁠ slot.

logical, whether to overwrite item with the same data_name in the ⁠@misc⁠ slot of object (default is FALSE).

object name.

name of the assay containing the raw data.

name of the assay containing the Cell Bender'ed data.

Seurat or LIGER object

Arguments passed to other methods

name to use for new meta data column. Default is "log10GenesPerUMI".

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning that function will abort if column with name provided to meta_col_name is present in meta.data slot.

assay to use in calculation. Default is "RNA". Note This should only be changed if storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

Seurat or LIGER object

Arguments passed to other methods

logical, whether to add percentage of counts belonging to mitochondrial/ribosomal genes to object (Default is TRUE).

logical, whether to add Cell Complexity to object (Default is TRUE).

logical, whether to add Top Gene Percentages to object (Default is TRUE).

logical, whether to add percentages of counts belonging to genes from of mSigDB hallmark gene lists: "HALLMARK_OXIDATIVE_PHOSPHORYLATION", "HALLMARK_APOPTOSIS", and "HALLMARK_DNA_REPAIR" to object (Default is TRUE).

logical, whether to add percentage of counts belonging to IEG genes to object (Default is TRUE).

logical, whether to add percentage of counts belonging to homoglobin genes to object (Default is TRUE).

logical, whether to addcell cycle scores and phase based on CellCycleScoring. Only applicable if species = "human". (Default is TRUE).

Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat, drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically generate patterns and features.

name to use for the new meta.data column containing percent mitochondrial counts. Default is "percent_mito".

name to use for the new meta.data column containing percent ribosomal counts. Default is "percent_ribo".

name to use for the new meta.data column containing percent mitochondrial+ribosomal counts. Default is "percent_mito_ribo".

name to use for new meta data column for Add_Cell_Complexity. Default is "log10GenesPerUMI".

name to use for new meta data column for Add_Top_Gene_Pct. Default is "percent_topXX", where XX is equal to the value provided to num_top_genes.

name to use for new meta data column for percentage of MSigDB oxidative phosphorylation counts. Default is "percent_oxphos".

name to use for new meta data column for percentage of MSigDB apoptosis counts. Default is "percent_apop".

name to use for new meta data column for percentage of MSigDB DNA repair counts. Default is "percent_dna_repair"..

name to use for new meta data column for percentage of IEG counts. Default is "percent_ieg".

name to use for the new meta.data column containing percent hemoglobin counts. Default is "percent_mito".

A regex pattern to match features against for mitochondrial genes (will set automatically if species is mouse or human; marmoset features list saved separately).

A regex pattern to match features against for ribosomal genes (will set automatically if species is in default list).

A regex pattern to match features against for hemoglobin genes (will set automatically if species is in default list).

A list of mitochondrial gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).

A list of ribosomal gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).

A list of hemoglobin gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).

logical, whether feature names in the object are gene names or ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

An integer vector specifying the size(s) of the top set of high-abundance genes. Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.

assay to use in calculation. Default is "RNA". Note This should only be changed if storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

returns list of all accepted values to use for default species names which contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and chicken). Default is FALSE.

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning that function will abort if column with name provided to meta_col_name is present in meta.data slot.

Seurat or LIGER object

Arguments passed to other methods

Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat, drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically generate hemo_pattern values.

name to use for the new meta.data column containing percent hemoglobin counts. Default is "percent_hemo".

A regex pattern to match features against for hemoglobin genes (will set automatically if species is mouse or human; marmoset features list saved separately).

A list of hemoglobin gene names to be used instead of using regex pattern.

logical, whether feature names in the object are gene names or ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning that function will abort if columns with any one of the names provided to hemo_name is present in meta.data slot.

returns list of all accepted values to use for default species names which contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and rhesus macaque). Default is FALSE.

Assay to use (default is the current object default assay).

Seurat or LIGER object

Arguments passed to other methods

Species of origin for given Seurat Object. If mouse, human, marmoset, zebrafish, rat, drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically generate mito_pattern and ribo_pattern values.

name to use for the new meta.data column containing percent mitochondrial counts. Default is "percent_mito".

name to use for the new meta.data column containing percent ribosomal counts. Default is "percent_ribo".

name to use for the new meta.data column containing percent mitochondrial+ribosomal counts. Default is "percent_mito_ribo".

A regex pattern to match features against for mitochondrial genes (will set automatically if species is mouse, human, zebrafish, rat, drosophila, rhesus macaque, or chicken; marmoset features list saved separately).

A regex pattern to match features against for ribosomal genes (will set automatically if species is mouse, human, marmoset, zebrafish, rat, drosophila, rhesus macaque, or chicken).

A list of mitochondrial gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).

A list of ribosomal gene names to be used instead of using regex pattern. Will override regex pattern if both are present (including default saved regex patterns).

logical, whether feature names in the object are gene names or ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning that function will abort if columns with any one of the names provided to mito_name ribo_name or mito_ribo_name is present in meta.data slot.

returns list of all accepted values to use for default species names which contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and chicken). Default is FALSE.

Assay to use (default is the current object default assay).

the species prefix in front of gene symbols in object if providing two species for multi-species aligned dataset.

data.frame containing the results of FindMarkers, FindAllMarkers, or other DE test data.frame.

the name of data.frame column corresponding to percent expressed in group 1. Default is Seurat default "pct.1".

the name of data.frame column corresponding to percent expressed in group 2. Default is Seurat default "pct.2".

logical. If the marker_dataframe already contains column named "pct_diff" whether to overwrite or return error message. Default is FALSE.

object name.

data.frame/tibble containing meta data or path to file to read. Must be formatted as either data.frame or tibble.

name of the column in seurat_object@meta.data that contains matching variables to join_by_meta in meta_data.

name of the column in meta_data that contains matching variables to join_by_seurat in seurat_object@meta.data.

logical, is it ok to add NA values to seurat_object@meta.data. Default is FALSE. Be very careful if setting TRUE because if there is error in join operation it may result in all ⁠@meta.data⁠ values being replaced with NA.

logical, if there are shared columns between seurat_object@meta.data and meta_data should the current seurat_object@meta.data columns be overwritten. Default is FALSE. This parameter excludes values provided to join_by_seurat and join_by_meta.

Seurat or LIGER object.

Arguments passed to other methods

An integer vector specifying the size(s) of the top set of high-abundance genes. Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.

name to use for new meta data column. Default is "percent_topXX", where XX is equal to the value provided to num_top_genes.

Logical. Whether to overwrite existing an meta.data column. Default is FALSE meaning that function will abort if column with name provided to meta_col_name is present in meta.data slot.

logical, whether to print messages with status updates, default is TRUE.

assay to use in calculation. Default is "RNA". Note This should only be changed if storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

DFrame output from barcodeRanks.

point size for plotting, default is 6.

Title for plot, default is "Barcode Ranks".

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(1024, 1024).

numerical value at which to add vertical line designating estimated empty droplet plateau (default is NULL).

extra arguments passed to ggplot2::theme().

Seurat object name.

vector of genes to check.

logical. Whether to print message to console if alternate case features are found in addition to inclusion in returned list. Default is TRUE.

logical. Whether to return vector of alternate case features. Default is TRUE.

Name of assay to pull feature names from. If NULL will use the result of DefaultAssay(seurat_object).

name of data.frame created using CellBender_Feature_Diff.

threshold to use for feature plotting. Resulting plot will only contain features which exhibit percent change >= value. Default is 25.

Number of features to plot. Will ignore pct_diff_threshold and return plot with specified number of features. Default is NULL.

logical, whether or not to label the features that have largest percent difference between raw and CellBender counts (Default is TRUE).

Number of features to label if label = TRUE, (default is 20).

Minimum number of raw counts per feature necessary to be included in plot labels (default is 1)

logical, whether to use geom_text_repel to create a nicely-repelled labels; this is slow when a lot of points are being plotted. If using repel, set xnudge and ynudge to 0, (Default is TRUE).

A custom set of features to label instead of the features most different between raw and CellBender counts.

logical, whether to plot diagonal line with slope = 1 (Default is TRUE).

Plot title.

Label for x axis.

Label for y axis.

Amount to nudge X and Y coordinates of labels by.

Amount to nudge X and Y coordinates of labels by.

passed to geom_text_repel, exclude text labels that overlap too many things. Defaults to 100.

Color to use for text labels.

font face to use for text labels (“plain”, “bold”, “italic”, “bold.italic”) (Default is "bold").

text size for feature labels (passed to geom_text_repel).

color to use for shadow/outline of text labels (passed to geom_text_repel) (Default is white).

radius to use for shadow/outline of text labels (passed to geom_text_repel) (Default is 0.15).

Extra parameters passed to geom_text_repel through LabelPoints.

Seurat object name.

Name of the assay containing the raw count data.

Name of the assay containing the CellBender count data.

Name of raw count matrix in environment if not using Seurat object.

Name of CellBender count matrix in environment if not using Seurat object.

Seurat object name.

Cell names to highlight in named list.

Color to highlight cells.

non-highlighted cell colors (default is "lightgray")..

point size for both highlighted cluster and background.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Whether to label the highlighted meta data variable(s). Default is FALSE.

Variable in ⁠@meta.data⁠ to split the plot by.

logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.

Dimensionality Reduction to use (if NULL then defaults to Object default).

logical. If highlight_color = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Extra parameters passed toDimPlot.

LIGER object name.

logical, whether to return list with vector of cell barcodes for each dataset in LIGER object or to return single vector of cell barcodes across all datasets in object (default is FALSE; return vector of cells).

Arguments passed to other methods

LIGER object name.

name of meta data column to use, default is current default clustering.

logical, whether to return list with entries for cell barcodes for each identity in group.by or to return list of lists (1 entry per dataset and each ident within the dataset) (default is FALSE; return list)

Seurat object

column name in meta.data that contains sample ID information. Default is NULL and will use "orig.ident column

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value of current delimiter.

a single value of new delimiter desired.

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value of current delimiter.

a single value of new delimiter desired.

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value of current delimiter.

a single value of new delimiter desired.

A matrix

Type of checks to perform, choose one or more from:

• “infinite”: Emit a warning if any value is infinite

• “logical”: Emit a warning if any value is a logical

• “integer”: Emit a warning if any value is not an integer

• “na”: Emit a warning if any value is an NA or NaN

Seurat object name.

Name(s) (or number(s)) identity of cluster to be highlighted.

Color(s) to highlight cells. The default is NULL and plot will use scCustomize_Palette().

non-highlighted cell colors.

point size for both highlighted cluster and background.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Whether to label the highlighted cluster(s). Default is FALSE.

Feature to split plots by (i.e. "orig.ident").

logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.

size for plot title labels when using split.by.

Number of columns in plot layout. Only valid if split.by != NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Extra parameters passed to DimPlot.

Seurat object name.

meta data column to classify samples (default = "orig.ident").

Seurat object name.

Features to plot.

Variable in ⁠@meta.data⁠ to split the identities plotted by.

Color palette to use for plotting expression scale. Default is viridis::plasma(n = 20, direction = -1).

Minimum scaled average expression threshold (everything smaller will be set to this). Default is -2.

What scaled expression value to use for the middle of the provided colors_use_exp. By default will be set to value in middle of exp_color_min and exp_color_max.

Minimum scaled average expression threshold (everything smaller will be set to this). Default is 2.

Whether to plot average normalized expression or scaled average normalized expression. Only valid when split.by is provided.

Whether to print the quantiles of expression data in addition to plots. Default is FALSE. NOTE: These values will be altered by choices of exp_color_min and exp_color_min if there are values below or above those cutoffs, respectively.

specify color palette to used for identity labels. By default if number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

logical, whether to show colors for idents on the column/rows of the plot (default is TRUE).

How to rotate column labels. By default set to TRUE which rotates labels 45 degrees. If set FALSE rotation is set to 0 degrees. Users can also supply custom angle for text rotation.

if plot needs extra white space padding so no plot or labels are cutoff. The parameter accepts TRUE or numeric vector of length 4. If TRUE padding will be set to c(2, 10, 0 0) (bottom, left, top, right). Can also be customized further with numeric vector of length 4 specifying the amount of padding in millimeters. Default is NULL, no padding.

logical, whether to flip the axes of final plot. Default is FALSE; rows = features and columns = idents.

Value to use for k-means clustering on features Sets (km) parameter in ComplexHeatmap::Heatmap(). From ComplexHeatmap::Heatmap(): Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above.

Number of k-means runs to get a consensus k-means clustering for features. Note if feature_km_repeats is set to value greater than one, the final number of groups might be smaller than row_km, but this might mean the original row_km is not a good choice. Default is 1000.

Number of k-means runs to get a consensus k-means clustering. Similar to feature_km_repeats. Default is 1000.

Size of the feature labels. Provided to row_names_gp in Heatmap call.

Fontface to use for row labels. Provided to row_names_gp in Heatmap call.

color to use for heatmap grid. Default is NULL which "removes" grid by using NA color.

logical, whether to cluster and reorder feature axis. Default is TRUE.

logical, whether to cluster and reorder identity axis. Default is TRUE.

Size of the feature labels. Provided to column_names_gp in Heatmap call.

Size of the legend text labels. Provided to labels_gp in Heatmap legend call.

Size of the legend title text labels. Provided to title_gp in Heatmap legend call.

Location of the plot legend (default is "right").

Orientation of the legend (default is NULL).

logical, whether to show the color legend for idents in plot (default is TRUE).

logical, whether to show row names on plot (default is TRUE).

logical, whether to show column names on plot (default is TRUE).

Should the row names be on the "bottom" or "top" of plot. Default is "bottom".

Should the row names be on the "left" or "right" of plot. Default is "right".

Logical, whether to render in raster format (faster plotting, smaller files). Default is FALSE.

Logical, whether or not to return the Sum Squared Error Elbow Plot for k-means clustering. Estimating elbow of this plot is one way to determine "optimal" value for k. Based on: https://stackoverflow.com/a/15376462/15568251.

The maximum value of k to use for plot_km_elbow. Suggest setting larger value so the true shape of plot can be observed. Value must be 1 less than number of features provided. If NULL parameter will be set dependent on length of feature list up to elbow_kmax = 20.

Name of assay to use, defaults to the active assay.

Group (color) cells in different ways (for example, orig.ident).

Which classes to include in the plot (default is all).

Logical, Sets parameter of same name in ComplexHeatmap::Heatmap(). From ComplexHeatmap::Heatmap(): When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms. Default is TRUE.

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Sets seed for reproducible plotting (ComplexHeatmap plot).

Seurat object name.

name(s) of assays to convert. Default is NULL and will check with users which assays they want to convert.

value of what assay type to convert current assays to. #'

• Accepted values for V3/4 are: "Assay", "assay", "V3", or "v3".

• Accepted values for V5 are: "Assay5", "assay5", "V5", or "v5".

folder to be copied to GCP bucket.

GCP bucket path to copy to files.

folder to be copied to GCP bucket.

GCP bucket path to copy to files.

file path to raw data file(s).

type of source data (Default is "10X"). Alternatively can provide "Matrix" or "data.frame".

file path to directory to save file.

name prefix for output H5 file.

matrix file containing the cell bender correct counts.

matrix file contain the uncorrected Cell Ranger (or other) counts.

a key value to use specifying the name of assay. Default is "RAW".

value to supply to min.cells parameter of CreateSeuratObject. Default is 5.

value to supply to min.features parameter of CreateSeuratObject. Default is 200.

Extra parameters passed to CreateSeuratObject.

path to directory to save file. Default is current working directory.

name to use for annotation file. Function automatically adds file type ".csv" suffix. Default is "cluster_annotation".

Seurat object name.

Meta data column to split plots by.

single color to use for all plots or a vector of colors equal to the number of plots.

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

size for plot title labels.

number of columns in final layout plot.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Which dimensions to plot. Defaults to c(1,2) if not specified.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Extra parameters passed to DimPlot.

liger liger_object. Need to perform clustering before calling this function

Variable to be plotted. If NULL will plot clusters from liger@clusters slot. If combination = TRUE will plot both clusters and meta data variable.

Variable to split plots by.

colors to use for plotting by clusters. By default if number of levels plotted is less than or equal to 36 will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

colors to use for plotting by meta data (cell.data) variable. By default if number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

Adjust point size for plotting.

logical. Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (Default is TRUE).

Sets the seed if randomly shuffling the order of points.

What to label the x and y axes of resulting plots. LIGER does not store name of technique and therefore needs to be set manually. Default is "UMAP". (only valid for rliger < 2.0.0).

specify reduction to use when plotting. Default is current object default reduction (only valid for rliger v2.0.0 or greater).

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

logical. Whether or not to label the clusters. ONLY applies to plotting by cluster. Default is TRUE.

size of cluster labels.

logical. Whether to repel cluster labels from each other if plotting by cluster (if group_by = NULL or ⁠group_by = "cluster⁠). Default is FALSE.

logical. Whether to put a box around the label text (uses geom_text vs geom_label). Default is FALSE.

Color to use for cluster labels. Default is "black".

logical, whether to return patchwork displaying both plots side by side. (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Number of columns in plot layout. Only valid if split.by != NULL.

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Seurat object name.

color palette to use for plotting. By default if number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

Adjust point size for plotting.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Feature to split plots by (i.e. "orig.ident").

logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.

logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

logical, whether to add plot to returned layout with the number of cells per identity (or percent of cells per identity). Default is FALSE.

logical, if add_prop_plot = TRUE this parameter controls whether proportion plot shows raw cell number or percent of cells per identity. Default is FALSE; plots raw cell number.

logical, if add_prop_plot = TRUE this parameter controls whether to change x axis to log10 scale (Default is FALSE).

logical, if add_prop_plot = TRUE this parameter controls whether to label the bars with total number of cells or percentages; Default is FALSE.

logical. Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (Default is TRUE).

Sets the seed if randomly shuffling the order of points.

Whether to label the clusters. By default if group.by = NULL label = TRUE, and otherwise it is FALSE.

Sets size of labels.

Sets the color of the label text.

Whether to put a box around the label text (geom_text vs geom_label).

Which dimensions to plot. Defaults to c(1,2) if not specified.

Repel labels.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Number of columns in plot layout. Only valid if split.by != NULL.

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to DimPlot.

Number of colors to be generated.

Options are "alphabet", "alphabet2", "glasbey", "polychrome", "stepped", "ditto_seq", "varibow".

randomly shuffle the outputted palette. Most useful for varibow palette as that is normally an ordered palette.

random seed for the palette shuffle. Default = 123.

Seurat object name.

Features to plot.

Name of metadata variable (column) to group cells by (for example, orig.ident); default is the current active.ident of the object.

specify color palette to used. Default is viridis_plasma_dark_high.

logical. Whether to remove the x and y axis titles. Default = TRUE.

Rotate x-axis labels 45 degrees (Default is FALSE).

Rotate x-axis labels 45 degrees (Default is FALSE).

Rotate facet labels on grouped DotPlots by 45 degrees (Default is FALSE).

whether or not to flip and X and Y axes (Default is FALSE).

Extra parameters passed to DotPlot.

LIGER object name.

name of dimensionality reduction to pull

logical, whether to extract iNMF h.norm matrix instead of dimensionality reduction embeddings.

logical, return TRUE if valid reduction is present.

Arguments passed to other methods

list of matrices to split by modality

Seurat object

meta.data column to use as sample. Output data.frame will contain one row per level or unique value in this variable.

⁠@meta.data⁠ columns to keep in final data.frame. All other columns will be discarded. Default is NULL.

columns to discard in final data.frame. Many cell level columns are irrelevant at the sample level (e.g., nFeature_RNA, percent_mito).

• Default parameter value is NULL but internally will set to discard nFeature_ASSAY(s), nCount_ASSAY(s), percent_mito, percent_ribo, percent_mito_ribo, and log10GenesPerUMI.

• If sample level median values are desired for these type of variables the output of this function can be joined with output of Median_Stats.

• Set parameter to include_all = TRUE to prevent any columns from being excluded.

logical, whether or not to include all object meta data columns in output data.frame. Default is FALSE.

data.frame output from FindAllMarkers or similar analysis.

number of genes per group (e.g., cluster) to include in output list.

column name of marker_dataframe to group data by. Default is "cluster" based on FindAllMarkers.

column name of marker_dataframe to rank data by when selecting num_genes per group_by. Default is "avg_log2FC" based on FindAllMarkers.

column name of marker_dataframe that contains the gene IDs. Default is "gene" based on FindAllMarkers.

logical. Whether gene IDs are stored in rownames and should be moved to column. Default is FALSE.

Logical, whether or not to return filtered data.frame of the original markers_dataframe or to return a vector of gene IDs. Default is FALSE.

Logical, whether or not to name the vector of gene names that is returned by the function. If TRUE will name the vector using the column provided to group_by. Default is TRUE.

Logical, whether an unnamed vector should return only unique values. Default is FALSE. Not applicable when data_frame = TRUE or named_vector = TRUE.

liger or Seurat object.

Color palette to use for correlation values. Default is RColorBrewer::RdBu if positive_only = FALSE. If positive_only = TRUE the default is viridis. Users can also supply vector of 3 colors (low, mid, high).

logical, whether to add correlation values to plot result.

threshold for adding correlation values if label = TRUE. Default is 0.5.

size of correlation labels

Plot title.

Controls plotting full matrix, or just the upper or lower triangles. Accepted values are: "full" (default), "upper", or "lower".

logical, whether to limit the plotted values to only positive correlations (negative values set to 0); default is FALSE.

logical, whether to rotate the axes labels on the x-axis. Default is TRUE.

logical, whether to cluster the plot using hclust (default TRUE). If FALSE factors are listed in numerical order.

logical, whether to add rectangles around the clustered areas on plot, default is FALSE.

number of rectangles to add to the plot, default NULL.

color to use for rectangles, default MULL (will set color automatically).

Seurat object name.

Feature(s) to plot.

name of assay one. Default is "RAW" as featured in Create_CellBender_Merged_Seurat

name of assay two Default is "RNA" as featured in Create_CellBender_Merged_Seurat

list of colors or color palette to use.

optional, a second color palette to use for the second assay.

color to use for points below lower limit.

whether to move positive cells to the top (default = TRUE).

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Value to use as minimum expression cutoff. To set no cutoff set to NA.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Which layer to pull expression data from? Default is "data".

Number of columns in plot layout. If number of features > 1 then num_columns dictates the number of columns in overall layout (num_columns = 1 means stacked layout & num_columns = 2 means adjacent layout).

new alpha level to apply to expressing cell color palette (colors_use). Must be value between 0-1.

new alpha level to apply to non-expressing cell color palette (na_color). Must be value between 0-1.

Extra parameters passed to FeaturePlot.

Seurat object name.

Feature(s) to plot.

list of colors or color palette to use.

color to use for points below lower limit.

whether to move positive cells to the top (default = TRUE).

Adjust point size for plotting.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Value to use as minimum expression cutoff. This will be lowest value plotted use palette provided to colors_use. Leave as default value to plot only positive non-zero values using color scale and zero/negative values as NA. To plot all values using color palette set to NA.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Variable in ⁠@meta.data⁠ to split the plot by.

logical, whether to collect the legends/guides when plotting with split.by. Default is TRUE if one value is provided to features otherwise is set to FALSE.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.

Number of columns in plot layout.

Which layer to pull expression data from? Default is "data".

new alpha level to apply to expressing cell color palette (colors_use). Must be value between 0-1.

new alpha level to apply to non-expressing cell color palette (na_color). Must be value between 0-1.

logical, whether to label the clusters. Default is FALSE.

logical, whether to place feature labels on secondary y-axis as opposed to above legend key. Default is FALSE. When setting label_feature_yaxis = TRUE the number of columns in plot output will automatically be set to the number of levels in ⁠split.by'⁠

Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects.

Extra parameters passed to FeaturePlot.

Seurat object name.

First feature to plot.

Second feature to plot.

Cells to include on the scatter plot.

color for the points on plot.

Adjust point size for plotting.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Default is active ident.

Feature to split plots by (i.e. "orig.ident").

logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.

logical, whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. Default is TRUE.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

size for plot title labels. Does NOT apply if split_seurat = TRUE.

Display correlation in plot subtitle (or title if split_seurat = TRUE).

number of columns in final layout plot.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to FeatureScatter.

Name of input data. Currently only data of classes: Seurat, liger, data.frame, dgCMatrix, dgTMatrix, tibble are accepted. Gene_IDs must be present in rownames of the data.

vector of features to check.

logical. Whether or not to check if features are found if the case is changed from the input list (Sentence case to Upper and vice versa). Default is TRUE.

logical. Whether to print message to console if alternate case features are found in addition to inclusion in returned list. Default is TRUE.

logical. Whether message should be printed if all features are found. Default is TRUE.

logical. Whether to print message about features that are not found in current object. Default is TRUE.

logical. Whether list of found vs. bad features should still be returned if no features are found. Default is FALSE.

Name of assay to pull feature names from if data is Seurat Object. Default is NULL which will check against features from all assays present.

LIGER object name.

logical, whether to return list with vector of features for each dataset in LIGER object or to return single vector of unique features across all datasets in object (default is FALSE; return vector of unique features)

Arguments passed to other methods

Object of class Seurat or liger.

Arguments passed to other methods

LIGER/Seurat object name.

reduction name to pull loadings for. Only valid if supplying a Seurat object.

number of colors to return in palette.

LIGER object name.

Arguments passed to other methods

name of column in cellMeta slot to set as new default cluster/ident

path to parent directory (if multi_directory = TRUE) or directory containing all h5 files (if multi_directory = FALSE).

logical, whether or not all h5 files are in their own subdirectories or in a single directory (default is TRUE; each in own subdirectory (e.g. output from Cell Ranger)).

Either the file name of h5 file (if multi_directory = TRUE) or the shared suffix (if multi_directory = FALSE)

logical, whether the outputs to be read are from Cell Ranger multi as opposed to Cell Ranger count (default is FALSE). Only valid if multi_directory = FALSE.

logical, should files be read in parallel (default is FALSE).

Number of cores to use in parallel if parallel = TRUE.

file path to use for saving PDF output.

Name of PDF output file.

point size for plotting, default is 6.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(1024, 1024).

numerical values at which to add vertical line designating estimated empty droplet plateau (default is NULL). Must be vector equal in length to number of samples.

Additional parameters passed to Read10X_h5_Multi_Directory or Read10X_h5_GEO.

Seurat object name.

Color to highlight cells (default "navy"). Can provide either single color to use for all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.

non-highlighted cell colors.

point size for both highlighted cluster and background.

Dimensionality Reduction to use (if NULL then defaults to Object default).

directory file path and/or file name prefix. Defaults to current wd.

name suffix to append after sample name.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Extra parameters passed toDimPlot.

Seurat object name.

name of meta.data column containing sample names/ids (default is "orig.ident").

directory file path and/or file name prefix. Defaults to current wd.

name suffix to append after sample name.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

color scheme to use.

logical, whether or not to include plot legend, default is TRUE.

Value that should be used for plot title prefix if no_legend = TRUE. If NULL the value of meta_data_column will be used. Default is NULL.

Dimensionality Reduction to use (default is object default).

Dimensions to plot.

Adjust point size for plotting.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Extra parameters passed to DimPlot.

Seurat object name.

vector of features to plot. If a named vector is provided then the names for each gene will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.

color scheme to use.

color for non-expressed cells.

Value to use as minimum expression cutoff. To set no cutoff set to NA.

Variable in ⁠@meta.data⁠ to split the plot by.

whether to move positive cells to the top (default = TRUE).

logical. Whether to return plots to list instead of saving them to file(s). Default is FALSE.

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE).

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

numeric, number of features to plot on single page if single_pdf = TRUE. Default is 1.

Number of columns in plot layout (only applicable if single_pdf = TRUE AND features_per_page > 1).

logical, when plotting multiple features per page in single PDF whether to use landscape or portrait page dimensions (default is TRUE).

dpi for image saving.

Adjust point size for plotting.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

new alpha level to apply to expressing cell color palette (colors_use). Must be value between 0-1.

new alpha level to apply to non-expressing cell color palette (na_color). Must be value between 0-1.

Extra parameters passed to FeaturePlot.

Seurat object name.

Name of the column in seurat_object@meta.data slot to pull value from for highlighting.

The order in which to plot each level within meta_data_column if single_PDF is TRUE.

logical. Whether or not to sort and relevel the levels in meta_data_column if single_PDF is TRUE. Default is TRUE.

Color to highlight cells (default "navy"). Can provide either single color to use for all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.

non-highlighted cell colors.

point size for both highlighted cluster and background.

logical, whether or not to remove plot legend and move to plot title. Default is FALSE.

Value that should be used for plot title prefix if no_legend = TRUE. If NULL the value of meta_data_column will be used. Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

directory file path and/or file name prefix. Defaults to current wd.

name suffix to append after sample name.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Extra parameters passed toDimPlot.

Seurat object name.

number of PCs to plot (integer). Default is all dims present in PCA.

directory file path to save file.

prefix for file name (optional).

suffix for file name. Default is "PC_Loading_Plots".

Whether to return the plot list (Default is FALSE). Must assign to environment to save plot list.

Seurat object name.

vector of genes to plot. If a named vector is provided then the names for each gene will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.

color scheme to use.

color for non-expressed cells.

Adjust point size for plotting.

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Dimensionality Reduction to use (if NULL then defaults to Object default)

Create a single plot? If FALSE, a list with ggplot objects is returned.

NULL. This function only supports joint = FALSE. Leave as NULL to generate plots. To iterate joint plots see function: Iterate_Plot_Density_Joint.

Extra parameters passed to plot_density.

Seurat object name.

a list of vectors of genes to plot jointly. Each entry in the list will be plotted for the joint density. All entries in list must be greater than 2 features. If a named list is provided then the names for each list entry will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.

color scheme to use.

color for non-expressed cells.

Adjust point size for plotting.

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

dpi for image saving.

Dimensionality Reduction to use (if NULL then defaults to Object default)

Create a single plot? If FALSE, a list with ggplot objects is returned.

NULL. This function only supports joint = FALSE. Leave as NULL to generate plots. To iterate joint plots see function: Iterate_Plot_Density_Joint.

Extra parameters passed to plot_density.

Seurat object name.

vector of features to plot.

color palette to use for plotting. By default if number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

point size for plotting.

Name of one or more metadata columns to group (color) plot by (for example, orig.ident); default is the current active.ident of the object.

Feature to split plots by (i.e. "orig.ident").

directory file path and/or file name prefix. Defaults to current wd.

name suffix and file extension.

File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf.

the width (in inches) for output page size. Default is NULL.

the height (in inches) for output page size. Default is NULL.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

dpi for image saving.

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

liger object.

By default, labels cell names with dataset of origin (this is to account for cells in different datasets which may have same name). Other names can be passed here as vector, must have same length as the number of datasets. (default names(H)).

Whether to log-normalize raw data using Seurat defaults (default TRUE).

Whether to carry over variable genes (default TRUE).

Include dataset of origin in cluster identity in Seurat object (default FALSE).

logical. Whether to transfer additional metadata (nGene/nUMI/dataset already transferred) to new Seurat Object. Default is TRUE.

Name of dimensionality reduction technique used. Enables accurate transfer or name to Seurat object instead of defaulting to "tSNE".

Name to set for assay in Seurat Object. Default is "RNA".

what type of Seurat assay to create in new object (Assay vs Assay5). Default is NULL which will default to the current user settings. See Convert_Assay parameter convert_to for acceptable values.

logical, whether to add dataset names to the cell barcodes when creating Seurat object, default is FALSE.

logical, if add_barcode_names = TRUE should the names be added as prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).

The delimiter to use when adding dataset id to barcode prefix/suffix. Default is "_".

Seurat object name.

Column in meta.data slot to group results by (default = "orig.ident").

logical. Whether to include the default meta.data variables of: "nCount_RNA", "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI" in addition to variables supplied to mad_var.

Column(s) in ⁠@meta.data⁠ to calculate medians for in addition to defaults. Must be of class() integer or numeric.

integer value to multiply the MAD in returned data.frame (default is 2). Often helpful when calculating a outlier range to base of of median + (X*MAD).

Seurat object name.

Column in meta.data slot to group results by (default = "orig.ident").

logical. Whether to include the default meta.data variables of: "nCount_RNA", "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI" in addition to variables supplied to median_var.

Column(s) in ⁠@meta.data⁠ to calculate medians for in addition to defaults. Must be of class() integer or numeric.

list composed of multiple Seurat Objects.

A character vector of equal length to the number of objects in list_seurat. Appends the corresponding values to the start of each objects' cell names. See merge.

Merge the data slots instead of just merging the counts (which requires renormalization). This is recommended if the same normalization approach was applied to all objects. See merge.

Project name for the Seurat object. See merge.

list of matrices to merge.

a vector of sample ids to add as prefix to cell barcode during merge.

logical. Whether add_cell_ids should be added as prefix to current cell barcodes/names or as suffix to current cell barcodes/names. Default is TRUE, add as prefix.

The delimiter to use when adding cell id prefix/suffix. Default is "_".

list of matrices to merge.

a vector of sample ids to add as prefix to cell barcode during merge.

logical. Whether add_cell_ids should be added as prefix to current cell barcodes/names or as suffix to current cell barcodes/names. Default is TRUE, add as prefix.

The delimiter to use when adding cell id prefix/suffix. Default is "_".

Seurat object name.

Name of the column in seurat_object@meta.data slot to pull value from for highlighting.

Name of variable(s) within meta_data_name to highlight in the plot.

Color to highlight cells (default "navy").

non-highlighted cell colors.

point size for both highlighted cluster and background.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires split_seurat = TRUE.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Whether to label the highlighted meta data variable(s). Default is FALSE.

Variable in ⁠@meta.data⁠ to split the plot by.

logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.

Dimensionality Reduction to use (if NULL then defaults to Object default).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Extra parameters passed toDimPlot.

a data.frame contain meta.data.

Seurat or Liger object name.

vector of column names to check.

logical. Whether message should be printed if all features are found. Default is TRUE.

logical. Whether to print message about features that are not found in current object. Default is TRUE.

logical. Whether list of found vs. bad features should still be returned if no meta_col_names are found. Default is FALSE.

data.frame containing meta data.

object name.

logical, are barcodes present as column and should they be moved to rownames (to be compatible with Seurat::AddMetaData). Default is FALSE.

name of barcodes column in meta_data. Required if barcodes_to_rownames = TRUE.

valid position to move legend. Default is "right".

extra arguments passed to ggplot2::theme().

Whether to flip the order of colors.

Seurat Object.

A single dim to plot (integer).

a vector of colors (either named colors of hex codes).

logical, whether or not to numerically label the colors in output plot. Default is TRUE is number of colors in pal is less than 75 and FALSE is greater than 75.

Seurat object name.

Feature(s) to plot.

Expression threshold to use for calculation of percent expressing (default is 0).

Factor to group the cells by.

Factor to split the groups by.

logical (default = FALSE). Whether to calculate percent of expressing cells across the entire object as opposed to by cluster or by group_by variable.

Which layer to pull expression data from? Default is "data".

Assay to pull feature data from. Default is active assay.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use.

size of the dots plotted if group_by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Seurat object name.

Features to plot.

logical. Whether to return joint density plot. Default is FALSE.

default viridis palette to use (must be one of: "viridis", "magma", "cividis", "inferno", "plasma"). Default is "magma".

non-default color palette to be used in place of default viridis options.

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Create a single plot? If FALSE, a list with ggplot objects is returned.

Extra parameters passed to plot_density.

Seurat object name.

Features to plot.

default viridis palette to use (must be one of: "viridis", "magma", "cividis", "inferno", "plasma"). Default is "magma".

non-default color palette to be used in place of default viridis options.

Adjust point size for plotting.

Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.

Dimensionality Reduction to use (if NULL then defaults to Object default).

Extra parameters passed to plot_density.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable if group_by is not NULL.

size of the dots plotted if group_by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable if group_by is not NULL.

size of the dots plotted if group_by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Seurat object name.

Variable in meta.data slot to calculate and plot median values for.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable if group_by is not NULL.

size of the dots plotted if group_by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Seurat object name.

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

Column in meta.data slot to group results by (i.e. "Treatment").

List of colors or color palette to use. Only applicable if group_by is not NULL.

size of the dots plotted if group_by is not NULL. Default is 1.

Plot title.

Label for y axis.

Label for x axis.

Label for plot legend.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Seurat object name.

whether to plot a pie chart or bar chart; value must be one of "bar" or "pie". Default is "bar"

whether to plot bar chart as total cell counts or percents, value must be one of "percent" or "count". Default is "percent".

meta data column to classify samples (default = "ident" and will use active.ident.

meta data variable to use to split plots. Default is NULL which will plot across entire object.

number of columns in plot. Only valid if split.by is not NULL.

Rotate x-axis labels 45 degrees (Default is FALSE). Only valid if plot_type = "bar".

color palette to use for plotting.

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

name of the data.frame/tibble or path to CSV file containing cluster annotation.

name of column containing cluster names/numbers (default is "cluster").

name of column contain the cell type annotation (default is "cell_type").

path to the parent directory which contains all of the subdirectories of interest.

Seurat object name.

Feature from meta.data, assay features, or feature name shortcut to plot.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Feature to split plots by (i.e. "orig.ident").

number of bins to plot default is 250.

color to fill histogram bars, default is "dodgerblue".

Number of columns in plot layout.

optional, vector to use for plot title. Default is the name of the variable being plotted.

assay to pull features from, default is active assay.

return list of accepted default shortcuts to provide to features instead of full name.

Seurat object name.

First feature to plot.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering genes per cell.

Plot line a potential high threshold for filtering genes per cell.

Plot line a potential low threshold for filtering feature1 per cell.

Plot line a potential high threshold for filtering feature1 per cell.

numerical value for thickness of cutoff lines, default is NULL.

vector of colors to use for plotting by identity.

Adjust point size for plotting.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Default is ⁠@active.ident⁠.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Sets the seed if randomly shuffling the order of points (Default is 1).

Extra parameters passed to FeatureScatter.

Seurat object name.

First feature to plot.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering UMI per cell.

Plot line a potential high threshold for filtering UMI per cell.

Plot line a potential low threshold for filtering feature1 per cell.

Plot line a potential high threshold for filtering feature1 per cell.

numerical value for thickness of cutoff lines, default is NULL.

vector of colors to use for plotting by identity.

Adjust point size for plotting.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Default is ⁠@active.ident⁠.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Sets the seed if randomly shuffling the order of points (Default is 1).

Extra parameters passed to FeatureScatter.

Seurat object name.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering genes per cell.

Plot line a potential high threshold for filtering genes per cell.

Plot line a potential low threshold for filtering UMIs per cell.

Plot line a potential high threshold for filtering UMIs per cell.

numerical value for thickness of cutoff lines, default is NULL.

vector of colors to use for plotting by identity.

Name of continuous meta data variable to color points in plot by. (MUST be continuous variable i.e. "percent_mito").

The gradient color palette to use for plotting of meta variable (default is viridis "Plasma" palette with dark colors high).

Color to use for plotting values when a meta_gradient_low_cutoff is set (default is "lightgray").

Value to use as threshold for plotting. meta_gradient_name values below this value will be plotted using meta_gradient_na_color.

Cells to include on the scatter plot (default is all cells).

logical (default FALSE). Whether or not to return a plot layout with both the plot colored by identity and the meta data gradient plot.

logical, whether to plot the legend containing identities (left plot) when combination = TRUE. Default is TRUE.

Passes size of points to both FeatureScatter and geom_point.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Default is ⁠@active.ident⁠.

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 cells.

Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

Random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Sets the seed if randomly shuffling the order of points (Default is 1).

Extra parameters passed to FeatureScatter.

Seurat object name.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Numeric vector of length 1 or 2 to plot lines for potential low/high threshold for filtering.

Numeric vector of length 1 or 2 to plot lines for potential low/high threshold for filtering.

Numeric vector of length 1 or 2 to plot lines for potential low/high threshold for filtering.

The column name containing percent mitochondrial counts information. Default value is "percent_mito" which is default value created when using Add_Mito_Ribo().

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

Seurat object name.

Feature from Meta Data to plot.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot Title.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting

logical, whether to plot median for each ident on the plot (Default is FALSE).

logical, whether to plot boxplot inside of violin (Default is FALSE).

Shape size for the median is plotted.

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

Seurat object name.

Feature from Meta Data to plot.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot Title.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

Seurat object name.

Plot Title.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

logical, whether to plot boxplot inside of violin (Default is FALSE).

Shape size for the median is plotted.

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

Seurat object name.

The column name containing percent mitochondrial counts information. Default value is "percent_mito" which is default value created when using Add_Mito_Ribo().

Plot Title.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

Seurat object name.

Plot Title.

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); default is the current active.ident of the object.

Label for x axis.

Label for y axis.

Plot line a potential low threshold for filtering.

Plot line a potential high threshold for filtering.

numerical value for thickness of cutoff lines, default is NULL.

Point size for plotting.

logical, whether to plot median for each ident on the plot (Default is FALSE).

Shape size for the median is plotted.

logical, whether to plot boxplot inside of violin (Default is FALSE).

vector of colors to use for plot.

Rotate x-axis labels 45 degrees (Default is TRUE).

logical. Whether to change y axis to log10 scale (Default is FALSE).

Convert points to raster format. Default is NULL which will rasterize by default if greater than 100,000 total points plotted (# Cells x # of features).

logical. If colors_use = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Extra parameters passed to VlnPlot.

Seurat object

number of cells per ident to use in down-sampling. This value must be less than or equal to the size of ident with fewest cells. Alternatively, can set to "min" which will use the maximum number of barcodes based on size of smallest group.

The ident to use to group cells. Default is NULL which use current active.ident. .

logical, whether or not to return the results as list instead of vector, default is FALSE.

logical, if number of cells in identity is lower than num_cells keep the maximum number of cells, default is FALSE. If FALSE will report error message if num_cells is too high, if TRUE will subset cells with more than num_cells to that value and those with less than num_cells will not be downsampled.

random seed to use for downsampling. Default is 123.

Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsv files provided by 10X.

A vector of file prefixes/names if specific samples are desired. Default is NULL and will load all samples in given directory.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the file name of each sample.

Specify which column of genes.tsv or features.tsv to use for gene names; default is 2.

Specify which column of barcodes.tsv to use for cell names; default is 1.

Make feature names unique (default TRUE).

Remove trailing "-1" if present in all cell barcodes.

logical (default FALSE). Whether to use multiple cores when reading in data. Only possible on Linux based systems.

if parallel = TRUE indicates the number of cores to use for multicore processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

path to the parent directory which contains all of the subdirectories of interest.

path from the parent directory to count matrix files for each sample.

logical (default TRUE) sets the secondary path variable to the default 10X directory structure.

logical, whether samples were processed with Cell Ranger multi, default is FALSE.

a vector of sample directory names if only specific samples are desired. If NULL will read in subdirectories in parent directory.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the subdirectory name of each sample.

logical (default FALSE) whether or not to use multi core processing to read in matrices.

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

Extra parameters passed to Read10X.

Directory containing the .h5 files provided by 10X.

A vector of file prefixes/names if specific samples are desired. Default is NULL and will load all samples in given directory.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the file name of each sample.

a suffix and file extension shared by all samples.

logical (default FALSE). Whether to use multiple cores when reading in data. Only possible on Linux based systems.

if parallel = TRUE indicates the number of cores to use for multicore processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

Additional arguments passed to Read10X_h5

path to the parent directory which contains all of the subdirectories of interest.

path from the parent directory to count matrix files for each sample.

logical (default TRUE) sets the secondary path variable to the default 10X directory structure.

logical, whether samples were processed with Cell Ranger multi, default is FALSE.

name of h5 file (including .h5 suffix). If all h5 files have same name (i.e. Cell Ranger output) then use full file name. By default function uses Cell Ranger name: "filtered_feature_bc_matrix.h5". If h5 files have sample specific prefixes (i.e. from Cell Bender) then use only the shared part of file name (e.g., "_filtered_out.h5").

a vector of sample directory names if only specific samples are desired. If NULL will read in subdirectories in parent directory.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the subdirectory name of each sample.

logical (default FALSE). Whether or not to replace the barcode suffixes of matrices using Replace_Suffix.

a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE. See Replace_Suffix for more information. To remove all suffixes set new_suffix_list = "".

logical (default FALSE) whether or not to use multi core processing to read in matrices.

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

Extra parameters passed to Read10X_h5.

Path to h5 file.

Label row names with feature names rather than ID numbers (default TRUE).

Make feature names unique (default TRUE).

Name of the group within H5 file that contains count data. This is only required if H5 file contains multiple subgroups and non-default names. Default is NULL.

Name of the slot contain feature names/ids. Must be one of: "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".

path to the parent directory which contains all of the subdirectories of interest.

path from the parent directory to count matrix files for each sample.

logical (default TRUE). Will set the shared file name suffix custom_name is NULL.

if file name was customized in CellBender then this parameter should contain the portion of file name that is shared across all samples. Must included the ".h5" extension as well.

a vector of sample directory names if only specific samples are desired. If NULL will read in subdirectories in parent directory.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the subdirectory name of each sample. NOTE: unless sample_list is specified this will rename files in the order they are read which will be alphabetical.

Name of the group within H5 file that contains count data. This is only required if H5 file contains multiple subgroups and non-default names. Default is NULL.

Name of the slot contain feature names/ids. Must be one of: "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".

logical (default FALSE). Whether or not to replace the barcode suffixes of matrices using Replace_Suffix.

a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE. See Replace_Suffix for more information. To remove all suffixes set new_suffix_list = "".

logical (default FALSE) whether or not to use multi core processing to read in matrices.

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

Extra parameters passed to Read_CellBender_h5_Mat.

Directory containing the .h5 files output by CellBender.

logical (default TRUE). Will set the shared file name suffix if custom_name is NULL.

if file name was customized in CellBender then this parameter should contain the portion of file name that is shared across all samples. Must included the ".h5" extension as well.

a vector of sample names if only specific samples are desired. If NULL will read in all files within data_dir directory.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the subdirectory name of each sample.

Name of the group within H5 file that contains count data. This is only required if H5 file contains multiple subgroups and non-default names. Default is NULL.

Name of the slot contain feature names/ids. Must be one of: "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".

logical (default FALSE) whether or not to use multi core processing to read in matrices

how many cores to use for parallel processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

Extra parameters passed to Read_CellBender_h5_Mat.

Directory containing the files.

The file suffix of the individual files. Must be the same across all files being imported. This is used to detect files to import and their GEO IDs.

logical. Whether gene IDs are present in first column or in row names of delimited file. If TRUE will move the first column to row names before creating final matrix. Default is TRUE.

a vector of samples within directory to read in (can be either with or without file_suffix see full_names). If NULL will read in all subdirectories.

logical (default FALSE). Whether or not the sample_list vector includes the file suffix. If FALSE the function will add suffix based on file_suffix parameter.

a set of sample names to use for each sample entry in returned list. If NULL will set names to the directory name of each sample.

Is the barcode suffix a period and should it be changed to "-". Default (FALSE; barcodes will be left identical to their format in input files.). If TRUE "." in barcode suffix will be changed to "-".

logical (default FALSE). Whether to use multiple cores when reading in data. Only possible on Linux based systems.

if parallel = TRUE indicates the number of cores to use for multicore processing.

logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.

path to the parent directory which contains all of the subdirectories of interest or alternatively can provide single csv file to read and format identically to reading multiple files.

path from the parent directory to count "outs/" folder which contains the "metrics_summary.csv" file.

logical (default TRUE) sets the secondary path variable to the default 10X directory structure.

logical, whether or not metrics come from Cell Ranger count or from Cell Ranger multi. Default is FALSE.

a list of sample names (matching directory names) to import. If NULL will read in all samples in parent directory.

a set of sample names to use for each sample. If NULL will set names to the directory name of each sample.

path to the parent directory which contains all of the sub-directories of interest or path to single metrics csv file.

a list of sample names (matching directory names) to import. If NULL will read in all samples in parent directory.

a set of sample names to use for each sample. If NULL will set names to the directory name of each sample.

object name.

vector of genes to check.

logical. Whether message should be printed if all features are found. Default is TRUE.

logical. Whether to print message about features that are not found in current object. Default is TRUE.

logical. Whether list of found vs. bad features should still be returned if no features are found. Default is FALSE.

Object of class Seurat or liger.

Arguments passed to other methods

vector of new cluster names. Must be equal to the length of current default identity of Object. Will accept named vector (with old idents as names) or will name the new_idents vector internally.

optional, name to use for storing current object idents in object meta data slot.

optional, name to use for storing new object idents in object meta data slot.

logical, whether to overwrite columns in object meta data slot. if they have same names as old_ident_name and/or new_ident_name.

. See old_ident_name.

Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

a single value or vector of values representing current barcode suffix. If suffix is the same for all matrices/data.frames in list only single value is required.

a single value or vector of values representing new barcode suffix to be added. If desired suffix is the same for all matrices/data.frames in list only single value is required. If no suffix is desired set new_suffix = "".'

data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).

Grouping factor for the plot. Default is to plot as single group with single point per sample.

colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

size of the dots plotted if plot_by is not sample_id Default is 1.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

Title to use for the patchworked plot output.

logical. Whether to calculate and plot p-value comparisons when plotting by grouping factor. Default is FALSE.

Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).

Grouping factor for the plot. Default is to plot as single group with single point per sample.

colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

size of the dots plotted if plot_by is not sample_id Default is 1.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

logical. Whether to calculate and plot p-value comparisons when plotting by grouping factor. Default is FALSE.

Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).

Grouping factor for the plot. Default is to plot as single group with single point per sample.

colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

size of the dots plotted if plot_by is not sample_id Default is 1.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

Title to use for the patchworked plot output.

logical. Whether to calculate and plot p-value comparisons when plotting by grouping factor. Default is FALSE.

Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).

Grouping factor for the plot. Default is to plot as single group with single point per sample.

colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

size of the dots plotted if plot_by is not sample_id Default is 1.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

logical. Whether to calculate and plot p-value comparisons when plotting by grouping factor. Default is FALSE.

Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).

Grouping factor for the plot. Default is to plot as single group with single point per sample.

colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

size of the dots plotted if plot_by is not sample_id Default is 1.

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

logical. Whether to calculate and plot p-value comparisons when plotting by grouping factor. Default is FALSE.

Other variables to pass to ggpubr::stat_compare_means when doing significance testing.