rliger (version 2.2.1)

plot.factorGSEA: 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 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",
  ...
)

Value

ggplot object

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.