Question: How to add a custom chromosome labels in qqman R package?
0
gravatar for rimgubaev
15 months ago by
rimgubaev190
Russia/Moscow/Skoltech
rimgubaev190 wrote:

Hello everyone? I wonder if someone knows how to change the chromosome labels at qqman package? I am making a manhattan plot using manhattan function which adds numeric chromosome codes to the x-axis like this:

enter image description here

However, the species under study has 2 subgenomes (A and C) so the chromosome codes should look like that: A1, A2... and C1, C2... And the manhattan x-axis would be like that:

enter image description here

I didn't find the solution for such a problem, so please, help.

ADD COMMENTlink modified 15 months ago • written 15 months ago by rimgubaev190
3
gravatar for rimgubaev
15 months ago by
rimgubaev190
Russia/Moscow/Skoltech
rimgubaev190 wrote:

Looks like the answer was much closer. I just neded to add an chrlabs option and add a vector of new names! Thank you guys! The command would look like these:

manhattan(results.df, chr="Chr", bp="Pos", p="p", snp = "Marker", chrlabs = new.names)

Where new.names is a character vector of size equal to the number of the chromosomes.

ADD COMMENTlink written 15 months ago by rimgubaev190
2
gravatar for bernatgel
15 months ago by
bernatgel2.9k
Barcelona, Spain
bernatgel2.9k wrote:

Hi,

I don't know how to do that with qqman, but if you are willing to try another package, you can do that with karyoploteR.

You can use kpPlotManhattan on a custom genome for your species and it will use whatever chromosome names you specify. It's quite easy to customize and very flexible regarding their look and feel: you can highlight specific regions in different ways, overlay different plots (even multiple manhattans as in you second image, can remove the ideograms, etc...

enter image description here

ADD COMMENTlink written 15 months ago by bernatgel2.9k
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