Upset plot for overlapping ChIP-seq peaks: an alternative to Venn diagram

ChIP-seq-upset

Ming Tang

January 25, 2016

I am going to demonstrate how to make Upset plot using UpSetR package for ChIP-seq peaks. After running a peak-calling method for 3 samples, you want to compare how many peaks are overlapped in two samples and in three samples. People may draw venn diagram for this kind of problem, but when you have more than 3 samples, the venn diagram is hard to read.

# install it if you have not 
# install.packages("UpSetR")
library(UpSetR)
dummy<- data.frame(peak=c("peak_1", "peak_1", "peak_1","peak_2","peak_2","peak_3","peak_3","peak_4"),
                   sample=c("sample_1","sample_2","sample_3","sample_2","sample_3","sample_2","sample_3","sample_1"))

dummy

##     peak   sample
## 1 peak_1 sample_1
## 2 peak_1 sample_2
## 3 peak_1 sample_3
## 4 peak_2 sample_2
## 5 peak_2 sample_3
## 6 peak_3 sample_2
## 7 peak_3 sample_3
## 8 peak_4 sample_1

To get the format that UpsetR accepts, we have to “spread” the sample column to multiple columns. It is like to change a long format data to wide format. See here as well.

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(tidyr)

peaks<- dummy %>% mutate(value =1) %>% spread(sample, value, fill =0 )
peaks

##     peak sample_1 sample_2 sample_3
## 1 peak_1        1        1        1
## 2 peak_2        0        1        1
## 3 peak_3        0        1        1
## 4 peak_4        1        0        0

I noticed that one has to convert peaks(local data frame) back to data.frame for UpsetR to work. In this example, I did not convert the peaks to local data frame by tbl_df(peaks).

upset(peaks, order.by = "freq")