How to add coverage plots of 6 samples in Covid viral genome using circos like R packages
0
0
Entering edit mode
3.8 years ago
S AR ▴ 80

I have plotted the sars-cov genes in the first circle and now I want to add the base coverage of 6 samples in the inner circles but I'm unable to add multi tracks for the coverage from 6 samples. My code is below that will make 2 circles one is plotting whole chromosome of COVID and the inner circle is the genes in this chromosome:

Library(circos)
df = data.frame(
+     name  = c("ORF1a","ORF1b", "S",  "ORF3a", "E", "M", "ORF6", "ORF7ab", "ORF8", "N", "ORF10"),
+     start = c(265, 13467, 21562, 25392, 26244, 26522, 27201, 27393, 27893, 28273, 29557),
+     end   = c(13468, 21555, 25384, 26220, 26472, 27191, 27387, 27887, 28259, 29533, 29674))
> col_text <- "black"
> circos.par("track.height"=0.85,gap.degree=5,cell.padding=c(0,0,0,0))
> circos.genomicInitialize(df, tickLabelsStartFromZero = FALSE, major.by = 1000,axis.labels.cex = 0.35*par("cex"))
circos.track(ylim=c(0,1),panel.fun=function(x,y) {
+     chr=CELL_META$sector.index
+     xlim=CELL_META$xlim
+     ylim=CELL_META$ylim
+     circos.text(mean(xlim),mean(ylim),chr,cex=0.5,col=col_text,
+                 facing="bending.inside",niceFacing=TRUE)
+ },bg.col = c("#FF000040", "#00FF0040", "#0000FF40","#FF0000", "#800000", "#FFFF00","#808000", "#00FF00", "#008000","#00FFFF", "#008080"),bg.border=F,track.height=0.06)

Now how to add base coverage on each genomic positions? I have histogram for each base :

ncov  basePos  Depth
ncov   1            0
ncov   2            255
ncov   3            10
ncov   4            350
ncov   5            12
.
.
.
.
.
.
.
ncov  225860      1001

I have this coverage file for each 6 samples

My plot currently looks like this: Plot.png

Any help will be really appreciated.

Thanks SAR

R genomic data visualization • 660 views
ADD COMMENT

Login before adding your answer.

Traffic: 2556 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6