plot_gsea {vulcan} | R Documentation |
This function generates a GSEA plot from a gsea object
plot_gsea(gsea.obj, twoColors = c("red", "blue"), plotNames = FALSE, colBarcode = "black", title = "Running Enrichment Score", bottomYtitle = "List Values", bottomYlabel = "Signature values", ext_nes = NULL, omit_middle = FALSE)
gsea.obj |
GSEA object produced by the |
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 |
bottomYtitle |
String for the title of the bottom part of the plot |
bottomYlabel |
String for the label |
ext_nes |
Provide a NES from an external calculation |
omit_middle |
If TRUE, will not plot the running score (FALSE by default) |
Nothing, a plot is generated in the default output device
reflist<-setNames(-sort(rnorm(26)),LETTERS) set<-c('A','B','D','F') obj<-gsea(reflist,set,method='pareto') plot_gsea(obj)