Color label of rainfall plot drawn by KaryoploteR

Question

[FL512]

Thanks to the amazing package of KaryoploteR and a great tutorial website, I was able to make a rainfall plot. https://bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfall.html

However, one thing that I am suffering from making a perfect rainfall plot is color label is missing. I would like to know and visualize what color is what like C>A is yellow, C>G is red for example. Tutorial website states to ask a question to Biostars, I am posting my question here.

Thank you very much in advance.

Answer 1

[Philipp Bayer]

You can use the standard legend() command as outlined in this issue here: https://support.bioconductor.org/p/124328/

Minimal example based on https://bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfall.html :

library(karyoploteR)


somatic.mutations <- read.table(file="ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Pancreas/Pancreas_raw_mutations_data.txt", header=FALSE, sep="\t", stringsAsFactors=FALSE)
somatic.mutations <- setNames(somatic.mutations, c("sample", "mut.type", "chr", "start", "end", "ref", "alt", "origin"))

somatic.mutations <- split(somatic.mutations, somatic.mutations$sample)
sm <- somatic.mutations[["APGI_1992"]]
sm.gr <- toGRanges(sm[,c("chr", "start", "end", "mut.type", "ref", "alt")])
seqlevelsStyle(sm.gr) <- "UCSC"

variant.colors <- getVariantsColors(sm.gr$ref, sm.gr$alt)
kp <- plotKaryotype(plot.type=4)
kpPlotRainfall(kp, data = sm.gr, col=variant.colors)
uniq_cols <- variant.colors[!duplicated(variant.colors)]
legend(x = "bottomright", fill=uniq_cols, legend=names(uniq_cols))

Now you can customise the call to legend() in any way you like.

Looks like this:

[FL512]

Thank you very much for your response Phillip. Also, thank you for providing the reference website. It helps a lot. Now I can see the figure legend on my plot.

Thank you again!

[Philipp Bayer]

Good luck :)

[FL512]

By the way, it is weird to me but I see 7 colors in my plot. Green (T>G), black (C>G), purple (T>A), red (C>T), yellow (T>C), blue (C>A) and gray (blank, no information)

Has anyone been having a same problem with color legend? How come it happens since I only extracted columns of "Chr", "Start", "End", "Mut_type", "REF", "ALT" from loaded Txt file.

[FL512]

Uh,,

I removed all the INDEL from my samples and there are no more gray dot shown in the rainfall plot, which I was expected. However, still gray box exist in the figure legend.

Anyway, the source file downloaded from the website: https://bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfall.html has no problem at all for the plot, indicating this is something wrong with my sample file.

I will figure it out. Thank you.

[Philipp Bayer]

Good work! I reckon uniq_cols still has the color-less indel in it.

This is what mine looks like:

> uniq_cols
      T>C       C>T       C>A       C>G       T>G       T>A 
"#fbe800" "#e40611" "#4c64ae" "#000000" "#6eb529" "#bf4a96"

You might have another entry in there with ' ' or something like that. To remove:

uniq_cols[-c(1)]

or whatever the position of the empty gray is in your named vector uniq_cols.