SuperExactTest

Current version 1.0.7.1

Description

SuperExactTest is an R package for statistical testing and visualization of mult-set intersections.

Installation

SuperExactTest is available from CRAN so the simplest way to install in R is by running install.packages("SuperExactTest").

To install the latest update from here in github, run devtools::install_github("mw201608/SuperExactTest") in R.

Reference

Minghui Wang, Yongzhong Zhao, and Bin Zhang (2015) Efficient Test and Visualization of Multi-Set Intersections. Scientific Reports 5: 16923.

Vignette

Detailed description about the package and sample analysis code is available from vignette("set_html",package="SuperExactTest") (link) after installation.

Example

library(SuperExactTest)
set.seed(1234)
#generate random strings
n=400
r_strings <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
input=lapply(c(40,60,80,200),function(x,s) sample(s,x),s=r_strings)
Result=supertest(input,n=n)
#plot the intersections with a split y-axis
#show elements of the intersections with no more than 20 elements
#png('examples/ex1.png',width=2000,height=2000,res=300)
plot(Result, Layout="landscape", sort.by="size", keep=FALSE,
	bar.split=c(70,180), show.elements=TRUE, elements.cex=0.7,
	elements.list=subset(summary(Result)$Table,Observed.Overlap <= 20),
	show.expected.overlap=TRUE,expected.overlap.style="hatchedBox",
	color.expected.overlap='red')
#dev.off()

As of version 1.0.7, we can change the order of the intersection bars in a customized way through option sort.by. For example, let us switch the orders of the fourth and fifth bars in the above figure.

#First extract the intersection barcodes ordered by size
order1=names(sort(Result$overlap.sizes,decreasing=TRUE))
#Then switch the orders of the fourth and fifth element
order2=order1[c(1:3,5,4,6:length(order1))]
print(order1)
print(order2)
#Now plot with the new order
#png('examples/ex2.png',width=2000,height=2000,res=300)
plot(Result, Layout="landscape", sort.by=order2, keep=FALSE,
        bar.split=c(70,180), show.elements=TRUE, elements.cex=0.7,
        elements.list=subset(summary(Result)$Table,Observed.Overlap <= 20),
        show.expected.overlap=TRUE,expected.overlap.style="hatchedBox",
        color.expected.overlap='red')
#dev.off()

We can also flip the bars upside down using option flip.vertical=TRUE.

#png('examples/ex3.png',width=2000,height=2000,res=300)
plot(Result, Layout="landscape", sort.by=order2, keep=FALSE,
        bar.split=c(70,180), show.elements=TRUE, elements.cex=0.7,
        elements.list=subset(summary(Result)$Table,Observed.Overlap <= 20),
        show.expected.overlap=TRUE,expected.overlap.style="hatchedBox",
        color.expected.overlap='red',flip.vertical=TRUE)
#dev.off()

Show fold enrichment rather than overlp size on top of the bars (since v1.0.7.1).

#png('examples/ex4.png',width=2000,height=2000,res=300)
plot(Result, Layout="landscape", sort.by=order2, keep=FALSE,
        bar.split=c(70,180), show.elements=TRUE, elements.cex=0.7,
		show.fold.enrichment=TRUE,
		elements.list=subset(summary(Result)$Table,Observed.Overlap <= 20),elements.rot=45,
        show.expected.overlap=TRUE,expected.overlap.style="hatchedBox",
        color.expected.overlap='red')
#dev.off()