plot_multi_module_enr {scITD}

Generate gene set x ct_module heatmap showing co-expression module gene set enrichment results

Description

Generate gene set x ct_module heatmap showing co-expression module gene set enrichment results

Usage

plot_multi_module_enr(
  container,
  ctypes,
  modules,
  sig_thresh = 0.05,
  db_use = "TF",
  max_plt_pval = 0.1,
  h_w = NULL
)

Arguments

container

environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses

ctypes

character A vector of cell type names corresponding to the module numbers in mod_select, specifying the modules to compute enrichment for

modules

numeric A vector of module numbers corresponding to the cell types in ctype, specifying the modules to compute enrichment for

sig_thresh

numeric P-value threshold for results to include. Only shows a given gene set if at least one module has a result lower than the threshold. (default=0.05)

db_use

character The database of gene sets to use. Database options include "GO", "Reactome", "KEGG", "BioCarta", "Hallmark", "TF", and "immuno". More than one database can be used. (default="GO")

max_plt_pval

max pvalue shown on plot, but not used to remove rows like sig_thresh (default=.1)

h_w

numeric Vector specifying height and width (defualt=NULL)

Value

A ComplexHeatmap object of enrichment results.