plot_multi_module_enr: Generate gene set x ct_module heatmap showing co-expression...

In scITD: Single-Cell Interpretable Tensor Decomposition

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.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.