Can we plot SNPs on a circos plot ?

[Krithika-Bhuvan]

Is it possible to plot single nulcletotide polymorphisms (SNPs) on a circos plot ? A SNP has the same start and end position. For example, 1:207620289 (rs12081383) 1:207624395 (rs72644189)

[jokergoo]

Then you can draw them as points.

[Krithika-Bhuvan]

Hello, I tried that but it doesn't work.

I put the same location in the "start" and "end" points. I also tried with "start" and "start + 1 " . Both times the track was plotted but no points. It seems like it will only work with a region where "start" and "end" points are far apart. Is there any workaround for this that you can suggest ?

Thanks, Krithika

On Sat, Oct 15, 2022 at 11:34 AM Zuguang Gu @.***> wrote:

Then you can draw them as points.

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[jokergoo]

No, it works for any type of genomic intervals:

circos.initializeWithIdeogram(plotType = "axis")
bed = data.frame(chr = "chr1", start = 1e8, end = 1e8, value = 1)
circos.genomicTrack(bed, ylim = c(0, 2), panel.fun = function(gr, value, ...) circos.genomicPoints(gr, value))

Maybe you can send me some example dataset?