plot_gsea_dot: Plot GSEA hypergeometric test

In kueckelj/confuns: Convenience Functions

Plot GSEA hypergeometric test

Description

Plots p-value or FDR results of hyper geometrics tests.

Usage

plot_gsea_dot(object, ...)

## S3 method for class 'hyp'
plot_gsea_dot(
  object,
  n.gsets = 20,
  signif.val = "fdr",
  signif.threshold = 0.05,
  color.by = "fdr",
  size.by = "geneset",
  pt.size = 2,
  pt.color = "blue4",
  pt.clrsp = "plasma",
  remove = "MF.GO|RCTM|CC.GO|HM",
  replace = c("_", " "),
  ...
)

## S3 method for class 'list'
plot_gsea_dot(
  object,
  n.gsets = 20,
  signif.val = "fdr",
  signif.threshold = 0.05,
  color.by = "fdr",
  size.by = "geneset",
  pt.size = 2,
  pt.color = "blue4",
  pt.clrsp = "plasma",
  remove = "MF.GO|RCTM|CC.GO|HM",
  replace = c("_", " "),
  ...
)

## S3 method for class 'data.frame'
plot_gsea_dot(
  object,
  n.gsets = 20,
  signif.val = "fdr",
  signif.threshold = 0.05,
  alpha.by = NULL,
  alpha.trans = "identity",
  color.by = "fdr",
  color.trans = "identity",
  size.by = NULL,
  size.trans = "identity",
  pt.alpha = 0.9,
  pt.size = 2,
  pt.color = "blue4",
  pt.clrsp = "plasma",
  remove = "^.+?(?=_)",
  replace = c("_", " "),
  ...
)

Arguments

object	Any object for whose class a method has been defined.
...	Additional arguments given to scale_color_add_on().
n.gsets	Numeric value. Maximal number of gene sets whose results are plotted. The first n.sets are included starting with the one with the lowest significance value.
signif.val	Character value. Either 'pval' or 'fdr'.
signif.threshold	Numeric value. The maximum significance value a gene set can have to be included.
size.by	Character value or NULL. If character, the variable whose values are displayed by size. Either 'geneset', the number of genes the gene set contains, or 'overlap', the number of genes that overlapped between the provided gene signature and the gene set.
remove	Character value or NULL. If character, regular expression given to pattern of stringr::str_remove_all(). Used to adjust gene set names.
replace	Character vector of length 2 or NULL. If character vector, two regular expressions. First value is given to argument pattern and second is given to argument replacement of stringr::str_replace_all(). Used to adjust gene set names.

Value

A ggplot.

kueckelj/confuns documentation built on July 4, 2024, 4:53 p.m.