https://github.com/mw201608/superexacttest
Statistical testing and visualization of mult-set intersections
https://github.com/mw201608/superexacttest
intersection set statistics visualization
Last synced: 3 months ago
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Statistical testing and visualization of mult-set intersections
- Host: GitHub
- URL: https://github.com/mw201608/superexacttest
- Owner: mw201608
- Created: 2018-04-12T20:56:15.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2023-12-26T16:51:24.000Z (about 2 years ago)
- Last Synced: 2025-10-22T03:57:48.051Z (3 months ago)
- Topics: intersection, set, statistics, visualization
- Language: R
- Homepage:
- Size: 1.59 MB
- Stars: 29
- Watchers: 2
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
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README
## SuperExactTest [](https://cran.r-project.org/package=SuperExactTest) [](http://www.r-pkg.org/pkg/SuperExactTest) [](http://www.r-pkg.org/pkg/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.](https://www.nature.com/articles/srep16923)
### Vignette
Detailed description about the package and sample analysis code is available from `vignette("set_html",package="SuperExactTest")` ([link](examples/set_html.Md)) after installation.
### SuperExactTest shiny
A shiny application has been deployed at [shinyapps.io](https://network.shinyapps.io/SuperExactTest/) (see also [github](https://github.com/mw201608/SuperExactTest.shiny)), 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
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 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 = "plot_left")
vp2 <- viewport(layout.pos.col = 2, layout.pos.row = 1, name = "plot_right")
vps <- vpTree(vp0, vpList(vp1, vp2))
pushViewport(vps)
seekViewport("plot_left")
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("plot_right")
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()
```
