Question

How to add a color legend to plotKaryotype and kpPlotRegions ?

1

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Aditya ▴ 160

@aditya-7667

Last seen 2.4 years ago

Germany

karyoploteR::plotKaryotype is great and works fine - thank you, Bernat :-) :

kp <- karyoploteR::plotKaryotype('mm10')
granges1 <- GenomicRanges::GRanges(c('chr1', 'chr2'), c('100-200', '100-200'))
granges2 <- GenomicRanges::GRanges(c('chr3', 'chr4'), c('100-200', '100-200'))
karyoploteR::kpPlotRegions(kp, granges1, col = "red")
karyoploteR::kpPlotRegions(kp, granges2, col = "green")

But how do I add a color legend (explaining what green and red set are)?

karyoploter • 3.4k views

ADD COMMENT • link updated 5.2 years ago by bernatgel ▴ 150 • written 5.2 years ago by Aditya ▴ 160

score 3 · Accepted Answer · 2019-09-03

3

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bernatgel ▴ 150

@bernatgel-7226

Last seen 10 months ago

Spain

Hi Aditya,

You can use legend as you would use with any other plot.

kp <- karyoploteR::plotKaryotype('mm10')
granges1 <- GenomicRanges::GRanges(c('chr1', 'chr2'), c('100-200', '100-200'))
granges2 <- GenomicRanges::GRanges(c('chr3', 'chr4'), c('100-200', '100-200'))
karyoploteR::kpPlotRegions(kp, granges1, col = "red")
karyoploteR::kpPlotRegions(kp, granges2, col = "green")

legend(x = "bottomright", fill = c("red", "green"), legend = c("Ranges1", "Ranges2"))

That will give you something like this

enter image description here

I usually prefer them as a single line below the plot as in this image, although that would require a bit more of fiddling with the positions.

enter image description here

ADD COMMENT • link 5.2 years ago bernatgel ▴ 150

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Thank you Bernat, for brushing up my rusty base graphics knowledge, and making this great package!

May I ask one more question? Is it possible to store the Karyoplot object in a variable and print it to a plot later? This works for ggplot2 and grid. I thought it doesn't for base graphics, but with Karyoplot you seem to have found a way around.

ADD REPLY • link 5.2 years ago Aditya ▴ 160

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Hehe! glad you find it useful!

karyoploteR is pure base graphics and so it's not possible to store it in a variable to plot later. Actually, karyoploteR plays really bad with graphics composition packages such as grid or the base par(mfrow=(A,B)). This is something I'd like to improve in the future, but for now the combination of karyoplots with other plots must be done out of R.

ADD REPLY • link 5.2 years ago bernatgel ▴ 150

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Hi again,

I just found out you can use karyoploteR with grid, cowplot and patchwork using the package ggplotify.

You can find the code in this github issue.

enter image description here

ADD REPLY • link 5.2 years ago bernatgel ▴ 150

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Oh, that's pretty cool indeed! Thanks for sharing.

ADD REPLY • link 5.2 years ago Aditya ▴ 160