plot_go_heatmap: Construct Expression Set Class

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This function will take an input expression matrix and make an Expression Set Class

Usage

plot_go_heatmap(
  input,
  sig_val = "p.adjust",
  cutoff = 0.1,
  max_categories = 30,
  color_by = "sig",
  subset_group = F,
  prune = F,
  cutoff_jaccard = 1,
  word_similarity = 0.5,
  select_GO = NULL
)

Arguments

input	the input Go result from clusterProfiler
sig_val	p.adjust of pvalue
cutoff	the value to be included
max_categories	mox categories included
color_by	what the cells should be shaded by. "count" or "sig"
subset_group	table(input@compareClusterResult$group)
prune	If true will prune the resulting heatmap based on jaccard similarity
cutoff_jaccard	The jaccard similarity index of terms to create a new group
word_similarity	for groups of go terms, the fraction of the original terms that a given word must occur in

Details

This will take the output of a GO enrichment analysis or GSEA object from clusterProfiler and merge terms based on the overlap between the enriched genes

Examples

plot_go_heatmap(input = gsea_result)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.