Entering edit mode
6.3 years ago
nkuo
▴
30
Hi guys, I am very new to R and I am trying to create a bacterial chromosome circos plot with different lineage
I am able to use circos plot to create the layer using following code
library(circlize)
rv_tables = read.table('final.tsv', header = T, sep = '\t')
df = data.frame( name = rv_tables$Chromsome, start = c(rv_tables$start), end = c(rv_tables$stop))
circos.genomicInitialize(df)
the rv_tables looks like this
chromosome gene start stop lineage1 lineage2 lineage 3
ch1 gene1 1 10 1 1 1
ch1 gene2 11 20 0 1 1
ch1 gene3 21 30 1 0 1
then add track for each lineage with following code:
circos.track(ylim = c(0, 1), bg.border = "black", bg.col='#FF000040', panel.fun = function(x,y) { (what to put) }, track.height = 0.125)
but now I want to show that genes are present/absence in each track (lineage), with 1 as present and 0 as not present, how do I do that within the circos.track to make that happen
thank you