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Old 05-10-2019, 10:46 AM   #9
guri
Junior Member
 
Location: USA

Join Date: May 2019
Posts: 1
Default Upset error

hi,

I have tried using upset plot for three vcf files from different pipelines. I extracted the variant column (SNPs) and used these csv files (with one column) for R import. I have used this code:

set1 <- read.csv("set1.vcf", sep="")
set2 <- read.csv("set2.vcf", sep="")
set3 <- read.csv("set3.vcf", sep="")

set1 <- as.vector(set1$V1)
set2 <- as.vector(set2$v1)
set3 <- as.vector(set3$V1)

read_sets = list(set1_reads = set1,
set2_reads = set2,
set3_reads = set3)

upset(fromList(read_sets),
sets = c("set1_reads", "set2_reads", "set3_reads"),
number.angles = 20, point.size = 2.5, line.size = 1.5,
mainbar.y.label = "read intersection", sets.x.label = "read set size",
text.scale = c(1.5, 1.5, 1.25, 1.25, 1.5, 1.5), mb.ratio = c(0.65, 0.35),
group.by = "freq", keep.order = TRUE)

It gives an intersection plot but when the number of SNPs from upset plot are really low when I compared these with vcf-compare results using same vcf files. I am not sure why I am getting different numbers with upset plot.
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