gsea.dotplot.onecol: Plot GSEA results as a dotplot

In FerrenaAlexander/FerrenaBulkRNAseq: Pipeline for analysis of bulkRNAseq data

Plot GSEA results as a dotplot

Description

Visualize GSEA results with a dotplot. Dot color is given by normalized enrichment score; size is given by number of genes shared in both pathway and in dataset; and asterisks show significance.

Usage

gsea.dotplot.onecol(
  gseares,
  filter_nonsig_pathways = NULL,
  top_pathways = NULL,
  ntop = NULL,
  fix_long_pathway_names = NULL,
  pathwayfontsize = NULL,
  gsubpattern = NULL
)

Arguments

gseares	dataframe with output of FGSEA. the first list element output of gsea.results.
filter_nonsig_pathways	T/F, whether to show only signifcant pathways (FDR <0.25); default = F
top_pathways	T/F, whether to show only top significant pathways. will show top "ntop" pathways. default = T
ntop	integer. if top_pathways=T, how many pathways to show in each "direction" of NES. If set to 25, will show 50 total pathways (25 positive NES, 25 negative NES). default = 25.
fix_long_pathway_names	T/F. Add newlines to pathway names if they exceed 50 characters. will try not to split words, assuming words are separated by underscores.
pathwayfontsize	numeric. Font size for pathway names. default = 10.
gsubpattern	character. Set this if there is a very repeptive symbol or prefix in all the pathway names. Default is "HALLMARK_"

Value

a ggplot object.

FerrenaAlexander/FerrenaBulkRNAseq documentation built on Oct. 16, 2022, 8:18 a.m.