plot_fgseaRes: Plot one-tailed GSEA on one signature for multiple gene sets

In fossbert/binilib: Carlo's little helper

Description

This function generates a plot of the member genes of a given gene set on a given signature for multiple gene sets.

Usage

plot_fgseaRes(
  ges,
  geneSets,
  fgseaRes,
  ledge_only = FALSE,
  signatureNames = NULL,
  color = c("firebrick2", "royalblue"),
  strip_PWnames = TRUE,
  ...
)

Arguments

ges	gene expression signature, a named vector of Z-scores, t-statistics, or log2 fold changes
geneSets	a named list of character vectors representing the gene sets
fgseaRes	Output of fgsea, will be used to get NES and adjusted p values
ledge_only	Logical, whether to include all genes of gene set or only those in leading edge
signatureNames	Character vector of length 2, specifying the experimental conditions
color	Vector of two components indicating the colors for each part of the signature
strip_PWnames	Logical, whether to remove commonly used Pathway prefixes, e.g. HALLMARK
...	adjustment of cex for pathway names

Value

Nothing, a plot is generated in the default output device

fossbert/binilib documentation built on April 23, 2021, 10:31 p.m.