plot.overlap: Plot Overlap With Heatmap

In mw201608/GOtest: Gene Ontology and Set Enrichment Test

Plot Overlap With Heatmap

Description

This function plots the overlap with a heatmap.

Usage

plotOverlap(x, col.set1, col.set2, col.set1.size, col.set2.size, 
	col.overlap.size, col.FE, col.Pvalue, col.text, cex.text=1.0,
	cex.lab=1.0, cex.legend=1.0, main='', order.by.size=TRUE,
	max.log10.p=320, cluster.by=NULL, fill=c('count','FE','text'),
	colorLabels=FALSE, show.set.size=TRUE, set.order=NULL, ...)

Arguments

x	a data.frame of overlap analysis result.
col.set1	column id of set 1 in x; used in rows of the heatmap.
col.set2	column id of set 2 in x; used in columns of the heatmap.
col.set1.size	column id of set 1 size.
col.set2.size	column id of set 2 size.
col.overlap.size	column id of overlap size.
col.FE	column id of fold enrichment.
col.Pvalue	column id of P value.
col.text	column id of text string used for fill.
cex.text	magnitude of text size.
cex.lab	magnitude of lable size.
cex.legend	magnitude of legend text size.
main	title of the plot.
order.by.size	whether to sort the sets by size.
max.log10.p	maximum absolute log10 P value. Larger values will be fixed to this value.
cluster.by	one of NULL, 'P' and 'FE'. See Details.
fill	fill the cells with count, fold enrichment (FE) or text. NULL to turn off filling.
colorLabels	whether to color the set labels if the sets are named by colors.
show.set.size	whether to show set size in the row and column labels.
set.order	NULL or a list with two named vectors Set1 and Set2 which specify the odered element IDs of two sets.
...	additional arguments used in function labeledHeatmap2.

Details

A modified version of function labeledHeatmap from package WGCNA will be called to plot overlap in a heatmap. cluster.by specifies how to cluster the sets (either by 'P' value or 'FE'), and, if not NULL, it overrides order.by.size.

See Also

GOtest

Examples

##not run###

mw201608/GOtest documentation built on May 3, 2023, 11:49 a.m.