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

if (FALSE) {
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")
}