olBarplot: Bar plot for intersect sets

In tgirke/systemPipeR: systemPipeR: NGS workflow and report generation environment

Bar plot for intersect sets

Description

Generates bar plots of the intersect counts of VENNset and INTERSECTset objects generated by the overLapper function. It is an alternative to Venn diagrames (e.g. vennPlot) that scales to larger numbers of label sets. By default the bars in the plot are colored and grouped by complexity levels of the intersect sets.

Usage

olBarplot(x, mincount = 0, complexity="default", myxlabel = "default", myylabel="Counts", mytitle = "default", ...)

Arguments

x	Object of class VENNset or INTERSECTset.
mincount	Sets minimum number of counts to consider in the bar plot. Default mincount=0 considers all counts.
complexity	Allows user to limit the bar plot to specific complexity levels of intersects by specifying the chosen ones with an integer vector. Default complexity="default" considers all complexity levels.
myxlabel	Defines label of x-axis.
myylabel	Defines label of y-axis.
mytitle	Defines main title of plot.
...	Allows to pass on additional arguments to geom_bar from ggplot2. For instance, fill=seq(along=vennlist(x)) or fill=seq(along=intersectlist(x)) will assign a different color to each bar, or fill="blue" will color all of them blue. The default bar coloring is by complexity levels of the intersect sets.

Value

Bar plot.

Note

The functions provided here are an extension of the Venn diagram resources on this site: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Venn-Diagrams

Author(s)

Thomas Girke

See Also

overLapper, vennPlot

Examples

## Sample data: list of vectors with object labels
setlist <- list(A=sample(letters, 18), B=sample(letters, 16),
                C=sample(letters, 20), D=sample(letters, 22),
                E=sample(letters, 18), F=sample(letters, 22))

## 2-way Venn diagram
vennset <- overLapper(setlist[1:2], type="vennsets")
vennPlot(vennset)

## 3-way Venn diagram
vennset <- overLapper(setlist[1:3], type="vennsets")
vennPlot(vennset)

## 4-way Venn diagram
vennset <- overLapper(setlist[1:4], type="vennsets")
vennPlot(list(vennset, vennset))

## Pseudo 4-way Venn diagram with circles
vennPlot(vennset, type="circle")

## 5-way Venn diagram
vennset <- overLapper(setlist[1:5], type="vennsets")
vennPlot(vennset)

## Alternative Venn count input to vennPlot (not recommended!)
counts <- sapply(vennlist(vennset), length)
vennPlot(counts)

## 6-way Venn comparison as bar plot
vennset <- overLapper(setlist[1:6], type="vennsets")
olBarplot(vennset, mincount=1)

## Bar plot of standard intersect counts
interset <- overLapper(setlist, type="intersects")
olBarplot(interset, mincount=1)

## Accessor methods for VENNset/INTERSECTset objects
names(vennset)
names(interset)
setlist(vennset)
intersectmatrix(vennset)
complexitylevels(vennset)
vennlist(vennset)
intersectlist(interset)

## Coerce VENNset/INTERSECTset object to list
as.list(vennset)
as.list(interset)

## Pairwise intersect matrix and heatmap
olMA <- sapply(names(setlist), 
		function(x) sapply(names(setlist), 
		function(y) sum(setlist[[x]] %in% setlist[[y]])))
olMA
heatmap(olMA, Rowv=NA, Colv=NA)

## Presence-absence matrices for large numbers of sample sets
interset <- overLapper(setlist=setlist, type="intersects", complexity=2)
(paMA <- intersectmatrix(interset))
heatmap(paMA, Rowv=NA, Colv=NA, col=c("white", "gray")) 

tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.