plot.factorGSEA: GSEA plot for specific gene set and factor using factorGSEA...

In rliger: Linked Inference of Genomic Experimental Relationships

GSEA plot for specific gene set and factor using factorGSEA results

Description

GSEA plot for specific gene set and factor using factorGSEA results

Usage

## S3 method for class 'factorGSEA'
plot(
  x,
  y,
  geneSetName,
  useFactor,
  xTitleSize = 10,
  xTextSize = 8,
  yTitleSize = 10,
  yTextSize = 8,
  titleSize = 12,
  captionTextSize = 8,
  ESLineColor = "green",
  ESLinewidth = 1,
  hitsLineColor = "black",
  hitsLinewidth = 0.5,
  loadingBarColor = "grey",
  ...
)

Arguments

x	A factorGSEA object.
y	Not used, for S3 method convention.
geneSetName	A character string for the gene set name to plot.
useFactor	A character string (e.g. 'Factor_1') or just numeric index for the factor name to plot.
xTitleSize, yTitleSize	Numeric, size for x or y axis titles, respectively. Default 10.
xTextSize, yTextSize	Numeric, size for x or y axis text, respectively. Default 8.
titleSize	Numeric, size for the main plot title. Default 12.
captionTextSize	Numeric, size for the caption text. Default 8.
ESLineColor	Color for the enrichment score line. Default 'green'.
ESLinewidth	Numeric, line width for the enrichment score line. Default 1.
hitsLineColor	Color for the hits line. Default 'black'.
hitsLinewidth	Numeric, line width for the hits line. Default 0.5.
loadingBarColor	Color for the loading bar. Default 'grey'.
...	Not used.

Value

ggplot object

rliger documentation built on Aug. 27, 2025, 1:08 a.m.