plot_gsea.venn.auto: Plot a Venn diagram of overlaps between genesets from >= 2...

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

Plot a Venn diagram of overlaps between genesets from >= 2 GSEA runs across a range of thresholds. By default, this will plot 4 venn diagrams: top 50 up, top 50 down, FDR<0.25 up, FDR<0.25 down

Usage

plot_gsea.venn.auto(..., gsea.list = NULL, names = NULL, file = NULL,
  main = "", N = c(50), FDR = c(0.25), P = NULL, FWER = NULL)

Arguments

gsea.list	a list of GSEA objects
names	the GSEA run names for labelling the Venn diagram
file	the path to the output pdf file, or NULL.
main	the plot title
N	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
FDR	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
P	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
FWER	see gsea.filter. It doesn't make sense to do a Venn diagram on all genesets, so you need to filter to find the significant ones.
...	>=2 GSEA results; or

Value

none. prints a venn diagram

Author(s)

Mark Cowley

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.