LeadEdgeSampleHeatmap: LeadEdgeSampleHeatmap make a heatmap of average expression...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

LeadEdgeSampleHeatmap make a heatmap of average expression for top or leading edge genes returned by LeadEdgeTidySampleExprs

Description

LeadEdgeSampleHeatmap make a heatmap of average expression for top or leading edge genes returned by LeadEdgeTidySampleExprs

Usage

LeadEdgeSampleHeatmap(
  tidy.exprs.list,
  modulename,
  celltype_plot,
  metadata,
  metadata_annotate,
  sample_column,
  returnmat = FALSE,
  plotwidth = 5,
  plotheight = 8,
  savepath,
  savename
)

Arguments

tidy.exprs.list	the object returned by returned by TidySampleData or LeadEdgeTidySampleExprs which is created from metadata and the object returned by PseudobulkList (average expression prefered for visualization; else recommend e.g. first lapply(x, edgeR::cpm) to standardize the bulk data.
modulename	The name of the module to plot
celltype_plot	the name of the celltype to plot
metadata	cells x metadata dataframe
metadata_annotate	a vector of variables (columns) of sample level metadata to annotate on the heatmap. Must be categorical for each sample e.g. "age" but not "nUMI"
sample_column	the column in the metadata object corresponding to the sample labels, usually 'smaple'
returnmat	instead of making an annotated heatmap just return the matrix of averge values per sample of the module subset

Value

a pheatmap object

Examples

## Not run: 
scglmmr::LeadEdgeSampleHeatmap(tidy.exprs.list = le_expr,
                               modulename = "MODULENAME",
                               celltype_plot = "TCELL",
                               metadata = meta,
                               metadata_annotate = c('group', 'timepoint', 'age', 'gender'),
                               sample_column = 'sample',
                              returnmat = F,
                               savepath = figpath,
                              savename = "filename")

## End(Not run)

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.