plot.new has not been called yet about karyoploter HOT 6 CLOSED

Running your code works perfectly fine for me...

Err... are you running them in an Rmarkdown document? If so, instead of selecting and running each line individually, select the whole chunk (or at least from plotKaryotype until the the last plotting function) and run them at once.

If you are using a standard R script, did you close the plot after running plotKaryotype and before running kpDataBackground?

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Thank you for your response. I was able to run it successfully based on your response. Now I am having another issue where I want to plot the kpPlotGenes below the graph. I am using plot.type = 2 and am getting the following error:

Error in ccf(chr = c(chr, chr), x = 0, y = c(0, t.mark.height)) : 
  If x is not NULL, it have to have the same length as chr

Here is my code for your reference:

par(mar=c(1,1,1,1))
plot.new()
pp <- getDefaultPlotParams(plot.type = 3)
pp$data1max <- 10
pp$data2max <- 10
kp <- plotKaryotype(zoom = toGRanges(data.frame("chr1", 1, 1e6)),
                    plot.type = 3,
                    main = "",
                    plot.params = pp,
                    ideogram.plotter = NULL)
kpDataBackground(kp, data.panel = 1, col = "#FFFFFF")
kpAxis(kp, r1 = 10, ymin = 0, ymax = 10, numticks = 5, cex = 1, data.panel = 1, side = 1)
kpPlotGenes(kp, data = TxDb.Hsapiens.UCSC.hg19.knownGene, plot.transcripts = T, data.panel = 2, r0 = 1, r1 = 3)

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I can reproduce the problem.
I'll have to take a deeper look at it to see what's happening.

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Thank you so much for looking into this. I really appreciate all your help and your awesome package!

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Also, when I call kpPlotMarkers without calling kpPlotGenes, I get the following error:

Error in karyoplot$getDataPanelBoundingBox(data.panel) : 
  attempt to apply non-function

I ran a script that worked fine in karyoploteR version 1.4.2 (from Bioconductor), and am getting that error now.

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Ok, there where a cuople of bugs due to recent changes for Bioconductor release! Thanks for reporting this.

The newest version in github (1.9.2) should work now. If you have any other problem, please open an issue here so we can take a look

In any case, ploease bear in mind that using the github version (from branch "master"), you are using the devel version of the package and that things will regularly break. Release branches are also available in github (latest one is branch "RELEASE_3_8") so you can use this if you want a more stable (less cutting edge) version of the package (bug fixes have also been applied to that branch).

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