plot_gseacmp.barplot: Taking a gseacmp object (see gsea.compare.runs.1gmt), create...

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

Taking a gseacmp object (see gsea.compare.runs.1gmt), create barplots of the NES scores for each geneset

Usage

plot_gseacmp.barplot(x, fdr.thresh = 0.05, do.par = TRUE, sub = "",
  max.label.length = 13, col = "lightblue", las = 2, nrow = 3,
  ncol = 4, legend.pos = "none", label.bars = c("stars", "FDR", "none"),
  label.fun = pvalue.stars)

Arguments

x	a gseacmp object (see gsea.compare.runs.1gmt)
fdr.thresh	Only keep genesets where at least 1 result is < this threshold.
do.par	setup the plotting region? defaults to TRUE
sub	see ?title
max.label.length	max number of characters in a name. Middle characters will be replaced with ... to make up a name of at most max.label.length. Hint: choose an odd number.
col	the barplot's background colour. ?see barplot
las	see ?par
nrow	how many plots per page. Passed to par(mfrow) if do.par=TRUE
ncol	how many plots per page. Passed to par(mfrow) if do.par=TRUE
legend.pos	Where to put the legend ONLY on the first plot. Try "top" or "bottom"
label.bars	stars: statistically significant bars are labelled using stars. See label.fun
label.fun	Function used to work out how many stars to plot for each bar. Defaults to pvalue.stars.
FDR	the FDR value is written on the bar, only if FDR < 0.25
none	no FDR labelling is done.

Author(s)

Mark Cowley, 2009-03-23

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.