plot_gsea.leadingedge.barplot.auto: Function to automatically plot barplot's of filtered GSEA...

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

Description

Function to automatically plot barplot's of filtered GSEA data.

Usage

plot_gsea.leadingedge.barplot.auto(x, file = NULL, N = c(50),
  FDR = c(0.25), P = NULL, FWER = NULL, min.count = 2, horiz = FALSE,
  col = "blue", cex.names = 0.6, write.delim = FALSE, ...)

Arguments

x	a GSEA list
file	the path to an output PDF file. if NULL, then plots are printed to current device.
N	if not NULL, then choose the top N most significant genesets
FDR	if not NULL, then choose those genesets with FDR < the threshold
P	if not NULL, then choose those genesets with nominal P < the threshold
FWER	if not NULL, then choose those genesets with FWER < the threshold
min.count	filter out genes found in only a few genesets. min.count=2 is useful in practice.
horiz	logical: horizontal or vertical plot?
col	the colour of the bars
cex.names	the character expansion factor of the gene names. see plot
write.delim	logical: if TRUE, then write the data plotted as a tab delimited txt file, named file + ".txt". Default is FALSE. If file=NULL, then write.delim will be set to FALSE.
...	arguments passed to plot_gsea.leadingedge.barplot

Value

none. Generates a number of plots, either to a pdf if file!=NULL, or dev.cur

Note

Usually, I filter by up or down, by top 50, and by FDR<0.25. This generates 4 plots

Author(s)

Mark Cowley, 2010-10-14

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