I would like to make a circos-like plot to visualize SNPs only (with multiple tracks for SNPs attributes). It could be done either with python, R or I am happy to consider other languages.
So far, I have taken a look at the circlize R package.
However, I get the error "Range of the sector ('C') cannot be 0" when initializing the circos plot.
I believe that this error arises from the fact that I have discrete data (SNPs) instead of having data for all positions. Or maybe this is because I have some data points that are repeated.
I have simplified my data below and show the code that I have tried so far:
Sample Gene Pos read_depth Freq
1 A 20394 43 99
1 B 56902 24 99
2 A 20394 50 99
2 B 56902 73 99
3 A 20394 67 50
3 B 56902 20 99
3 C 2100394 21 50
install.packages("circlize")
library(circlize)
data <- read.table("test_circos.txt", sep='\t', header=TRUE)
circos.par("track.height" = 0.1)
circos.initialize(factors = data$Gene, x = data$Pos)
I would like to know whether it is possible to get a circos-like plot where each of my data points (7 in my example) is plotted as an individual data point without any other points being plotted, in the way of a discrete axis.
If it is of interest to anyone, I decided to do as follows:
'Gene'); new column 'Number':Sample Gene Pos depth Freq Number
1 A 20394 43 99 1
1 B 56902 24 99 1
2 A 20394 50 99 2
2 B 56902 73 99 2
3 A 20394 67 50 3
3 B 56902 20 99 3
3 C 2100394 21 50 1
chr - ID LABEL START END COLOUR
chr - A A 0 3 chr1
chr - B B 0 3 chr2
chr - C C 0 1 chr3
This means that my genes will have length equal to the number of SNPs identified in said genes and that each bp of the genes will represent one line (=SNP) in my SNP file.
I can then use circos as normal.
In the end, I chose circos because it seemed best documented, therefore easier to learn with the addition of appearing more flexible.