corto (version 1.2.4)

plot_gsea2: Plot 2-way GSEA results

Description

This function generates a GSEA plot from a gsea object

Usage

plot_gsea2(
  gsea.obj,
  twoColors = c("red", "blue"),
  plotNames = FALSE,
  title = "Running Enrichment Score",
  bottomTitle = "List Values",
  bottomYlabel = "Signature values",
  legside1 = NULL,
  legside2 = NULL
)

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, and of the barcodes

plotNames

Logical. Should the set names be plotted?

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 (FALSE by default)

legside1

String specifying the position of the first NES legend, for example "topright", "bottomleft". Default is NULL, letting the function automatically place it

legside2

String specifying the position of the second NES legend, for example "topright", "bottomleft". Default is NULL, letting the function automatically place it

Examples

reflist<-setNames(-sort(rnorm(1000)),paste0('gene',1:1000))
set1<-paste0('gene',sample(1:200,50))
set2<-paste0('gene',sample(801:1000,50))
obj<-gsea2(reflist,set1,set2,method='pareto',np=1000)
plot_gsea2(obj)