corto (version 1.2.4)

plot_gsea: 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
)

Value

Nothing, a plot is generated in the default output device

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)

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)