plot.gsea2: Plot 2-tailed enrichment results

Description Usage Arguments Value

View source: R/plot_gsea.R

Description

This function generates a plot of the GSEA running sums of two gene sets on a given signature.

Usage

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## S3 method for class 'gsea2'
plot(
  gsea2,
  color = c("cornflowerblue", "salmon"),
  legend = TRUE,
  legNames = c("Targets", "pos", "neg"),
  main = "",
  plotSignature = FALSE,
  signatureNames = NULL,
  signatureType = NULL,
  ledge = TRUE,
  fixY = NULL,
  ...
)

Arguments

gsea2

gsea2 object as returned from gsea2T

color

Vector of two components indicating the colors for the negative and positive parts of the regulon

legend

Logical on whether to draw a legend explaining the two parts of the regulon

legNames

Character, defaults to Targets, pos and neg

main

Character vector given as argument for convenience

plotSignature

Logical whether to include a graph on the signature (e.g. t-statistics)

signatureNames

Character vector indicating the conditions being compared. Defaults to NULL. Otherwise a charater vector of length two.

signatureType

Character to indicate the type of gene level statistic (e.g. t-statistic).

ledge

logical whether to plot the leading edge line

fixY

numeric vector specyfying y-axis limits, defaults to NULL Defaults to NULL which will yield a 'signature score' label.

...

Given for compatibility to the plot generic function

Value

Nothing, a plot is generated in the default output device


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