karyoploteR error for custom genome about karyoploter HOT 5 CLOSED

Hi,
Thanks for your reply.
It's working when adjusting the scripts sequence. The kpPlotDensity function should be followed to plotKaryotype.

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Hi @tiramisutes,

I'll take a look at it.

Could it be that you closed the plot created by plotKaryotype before executing kpPlotDensity? all plottig functions assume that a plot is active and they never create a new one.

And could you tell if you are using Bioconductor 3.7 or the 3.8 released just yesterday? (the ouput from sessionInfo() would be perfect)

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Hi,
I find in the mycytobands.txt file the only accepted colors are gneg, gpos25, gpos75, gpos100, gvar, acen and stalk. How can I set the color by myself?

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If you want to change the color of the standard cytobands you can use the color.table argument in kpAddCytobands to give a named vector of colors.

Using custom named cytobands is not supported in the current version but it's in the TODO list. Meanwhile, you can force it in a not very elegant way:

• The cytoband names MUST be in a column called gieStain, but they can actually be whatever you want
• Build a color table matching your names

Something like this will create a ranbow colored genome

library(karyoploteR)
kp <- plotKaryotype(ideogram.plotter = NULL)

cytobands <- unlist(tileGenome(tilewidth = 10e6, seqlengths = kp$chromosome.lengths))

cytobands$gieStain <- paste0("color", as.character(seq_along(cytobands)))

color.table <- rainbow(length(cytobands))
names(color.table) <- paste0("color", as.character(seq_along(cytobands)))

kp$cytobands <- cytobands #This is needed because kpAddCytobands does not accept a cytobands parameter
kpAddCytobands(kp, color.table = color.table)

If what you actually want is to highlight certain regions in the genome, you can combine kpRect with the new (released last week with Bioconductor 3.8) data.panel="ideogram" to plot anything ON the ideogram itself

Hope this helps

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@bernatgel I am really sorry but I can't quite figure this out. I am trying to color a specific cytoband and the color would depend on the cytoband names. I tried making a cytoband color dataframe that would match a color to a given cytoband name. I also did not catch why we need to paste color values under the gieStain column; particularly this line of code cytobands$gieStain <- paste0("color", as.character(seq_along(cytobands)))? What should i do if I want a particular color for a specific cytoband present in multiple chromosomes? Sorry if this comes as stupid.

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