plot_gsea: Plot GSEA results

In federicogiorgi/corto: Inference of Gene Regulatory Networks

Plot GSEA results

Description

This function generates a GSEA plot from a gsea object

Usage

plot_gsea(
  gsea.obj,
  twoColors = c("red", "blue"),
  plotNames = FALSE,
  colBarcode = "black",
  title = "Running Enrichment Score",
  bottomTitle = "List Values",
  bottomYlabel = "Signature values",
  ext_nes = NULL,
  ext_pvalue = NULL,
  ext_es = NULL,
  omit_middle = FALSE
)

Arguments

gsea.obj	GSEA object produced by the gsea function
twoColors	the two colors to use for positive[1] and negative[2] enrichment scores
plotNames	Logical. Should the set names be plotted?
colBarcode	The color of the barcode
title	String to be plotted above the Running Enrichment Score
bottomTitle	String for the title of the bottom part of the plot
bottomYlabel	String for the Y label of the bottom plot
ext_nes	Provide a NES from an external calculation
ext_pvalue	Provide a pvalue from an external calculation
ext_es	Provide an ES from an external calculation
omit_middle	If TRUE, will not plot the running score (FALSE by default)

Value

Nothing, a plot is generated in the default output device

Examples

reflist<-setNames(-sort(rnorm(1000)),paste0('gene',1:1000))
set<-paste0('gene',sample(1:200,50))
obj<-gsea(reflist,set,method='pareto',np=1000)
plot_gsea(obj)

federicogiorgi/corto documentation built on April 24, 2023, 1:23 a.m.