SuperExactTest

Current version 1.1.2

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.

SuperExactTest shiny

A shiny application has been deployed at shinyapps.io (see also github), allowing users to run and visualize SuperExactTest analysis online.

Examples

1 Show selected overlapping elements

``` library(SuperExactTest) set.seed(1234)

generate random strings

n=400 rstrings <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE)) input=lapply(c(40,60,80,200),function(x,s) sample(s,x),s=rstrings) Result=supertest(input,n=n)

Plot the intersections with a split y-axis and

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()

```

Assign discrete colors to denote the sets that are involved in each intersection by setting color.on to NULL or a vector of colors. ```

png('examples/ex1color.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', color.on = NULL)

dev.off()

```

2 Sort and/or subset intersection bars for plotting

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', color.on = NULL)

dev.off()

```

With this option sort.by, we can also show a subset of the intersection bars easily. Eg, let us plot the 10 largest overlaps. ``` order3=order1[1:10]

png('examples/ex2b.png',width=2000,height=2000,res=300)

plot(Result, Layout="landscape", sort.by=order3, 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', color.on = NULL)

dev.off()

```

3 Flip the bars upside down

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', color.on = NULL, flip.vertical=TRUE)

dev.off()

```

4 Show fold enrichment

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', color.on = NULL)

dev.off()

```

5 Place multiple SuperExactTest plots on the same page

We can combine multiple SuperExactTest plots on the same page by setting new.gridPage = FALSE. For example, to arrange two SuperExactTest figures side by side, we can: ```

png('examples/ex5.png',width=4000,height=2000,res=300)

grid.newpage() vp0 <- viewport(layout = grid.layout(1, 2)) vp1 <- viewport(layout.pos.col = 1, layout.pos.row = 1, name = "plotleft") vp2 <- viewport(layout.pos.col = 2, layout.pos.row = 1, name = "plotright") vps <- vpTree(vp0, vpList(vp1, vp2)) pushViewport(vps) seekViewport("plotleft") plot(Result, Layout="landscape", sort.by='size', keep=FALSE, bar.split=c(70,180), show.fold.enrichment=TRUE, show.expected.overlap=TRUE, expected.overlap.style="hatchedBox", color.expected.overlap='red', color.on = NULL, title = 'Figure A. Landscape layout', new.gridPage = FALSE) seekViewport("plotright") plot(Result, Layout="circular", sort.by='size', keep=FALSE, show.expected.overlap=TRUE,expected.overlap.style="hatchedBox", color.expected.overlap='red', color.on = NULL, title = 'Figure B. Circular layout', new.gridPage = FALSE)

dev.off()

```