catplot.GSEA: Function to generate CAT plots for >= 2 GSEA comparisons

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

Description

This function expects all GSEA runs to be generated vs the same gmt file, and with no filtering done. Aside from the filtering upon geneset size that GSEA performs, there should be a large overlap in terms of genesets

Usage

catplot.GSEA(..., gsea.list = NULL, labels = LETTERS,
  legend.pos = "bottomright", proportion = FALSE, FDRthresh = 1.01,
  main = "", method = c("1-vs-all", "all-pairs"))

Arguments

gsea.list	an optional list of >= 2 GSEA objects. This overrides ...
labels	the name of of each GSEA run. must be same length as ..., or gsea.list.
legend.pos	where to add the names legend. default = “bottomright”, set to “none” to disable
proportion	if TRUE, x-axis is proportion of all genesets, if FALSE (default), the number of genesets is plotted.
FDRthresh	If you'd like the pch to change depending on which of A or B is significant, then choose a threshold of 0.25 for example. Pch will change depending on whether A and B are both significant, only one is significant, or neither are.
main	the plot title.
method	“1-vs-all” means compare the first GSEA run to all subseqent runs; “all-pairs” plots all pairwise comparisons of genesets.
...	at least 2 GSEA objects, or:

Author(s)

Mark Cowley, 2008-12-08 (edited date)

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