gsva_plot: Run ssGSEA and make a plot

In kevincjnixon/BinfTools: Useful functions for standard analyses

Run ssGSEA and make a plot

Description

A function to run an ssGSEA analysis using normalized counts and create a plot with pairwise comparisons

Usage

gsva_plot(
  counts,
  geneset,
  method = "ssgsea",
  stat.test = "t-test",
  condition,
  con = NULL,
  title = "ssGSEA",
  compare = NULL,
  col = "Dark2",
  style = "violin",
  sinaPoint = TRUE,
  showStat = TRUE,
  retRes = FALSE,
  textsize = NULL,
  retGP = FALSE
)

Arguments

counts	Normalized count matrix - preferably z-score normalized by row. E.g. t(scale(t(counts(dds, normalized=TRUE))))
geneset	List with length > 1 of character vectors indicating gene sets of interest. Can be created using qusage::read.gmt("geneset.gmt")
method	Method to employ in estimation of gene-set enrichment scores. One of "ssgsea","gsva","zscore","plage". Default is "ssgsea
stat.test	Test to employ in comparison of enrichment scores across conditions. Can only be "t-test" or "wilcoxon". Default is "t-test".
condition	Character vector of conditions in the same order they appear as columns in 'counts'.
con	Character indicating the control condition (Condition to be plotted first). Default is NULL.
title	Character vector indicating the title of the plot
compare	List of character vectors (each of length 2) indicating the pairwise comparisons to be made between conditions. Leave NULL for all comparisons to be made
col	Character indicating the RColorBrewer palette name or list of colours (hex, name, rgb()) to be used. Default is "Dark2".
style	Character indicating the style of plot ("violin", "box"). Defaults to "violin".
sinaPoint	Boolean indicating if sina points should be shown. Only when style="violin".
showStat	Boolean indicating if p-values should be plotted on figure
retRes	Boolean indicating if GSVA results should be returned. Default=FALSE. If both retRes and retGP are TRUE, only GSVA results will be returned.
textsize	Numeric indicating text size for plot. Leave NULL for default.
retGP	Boolean indicating if ggplots2 object should be returned for further editing. Default=FALSE.

Value

Violin or box plot of normalized enrichment scores for genesets between conditions

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.