How to generate an Upset plot in R to plot the shared variants between cell free DNA samples

Question

[sainavyav22]

Hello,

I have cell free DNA of 5 samples in VCF file format, I want to plot the shared variants between all the samples in an Upset plot. Which parameters do I need to consider as input and how to convert them into binary format. I have converted my files into tsv format.

This is the header of my VCF file:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1_P-gDNA   S1_P-cfDNA  NORMAL   cfDNA

Could some one please help with this?

Thanks.

Answer 1

[zx8754]

Try this example:

library(UpSetR)

#example input, 4 samples, 250 variants
set.seed(1); d <- data.frame(matrix(sample(c("0|0", "0|1", "0|1", "1|1"), 1000, 
                                           replace = TRUE), ncol = 4))
head(d)
#    X1  X2  X3  X4
# 1 0|0 0|0 0|1 0|1
# 2 1|1 1|1 0|1 0|1
# 3 0|1 0|1 0|1 1|1
# 4 0|0 0|0 0|0 0|1
# 5 0|1 0|0 0|0 1|1
# 6 0|0 0|1 0|1 0|1

variants <- seq(nrow(d))

# subset variants that have "1|1", update as needed
dl <- lapply(d, function(i) variants[ grepl("1|1", i, fixed = TRUE) ])
# lengths(dl)
# X1 X2 X3 X4 
# 57 66 66 61 

upset(fromList(dl))

[sainavyav22]

It worked, Thank you very much!