Hi
I am using the karyoplotR . I have genomics position of one chromosome that I want to diaply their interaction. Therefore I installed karyoplotR and run demo code which mainly uses links.
library(karyoploteR)
start.regs <- toGRanges(data.frame("chr1", 20e6, 30e6))
end.regs <- toGRanges(data.frame("chr3", 50e6, 55e6))
kp <- plotKaryotype()
kpPlotLinks(kp, data=start.regs, data2=end.regs)
But I am getting error while running last line of code kpPlotLinks(kp, data=start.regs, data2=end.regs) and error is
Error in kpPlotLinks(kp, data = start.regs, data2 = end.regs) :
could not find function "kpPlotLinks"
I checked the functions belongs to karyoploteR using library(help="karyoploteR") and did not find any such function. But this code is available at https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotLinks/PlotLinks.html .
Any idea how to show interaction within genomics positions using this package? I know circos, but I want to display linear chromosome therefore I opted this package.
All suggestions will be appreciated
Thank you in advance
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Omics data mining
1 answer
Just for future reference, the problem in this case was that the version of karyoploteR was an old one, from before the kpPlotLinks function was added. The karyoploteR tutorial page content always refers to the latest release version of the package.
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I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
In addition, please use sensible tags. This question doesn't have anything related to 'snp' and 'rnaseq'. Tags are useful if you want developers to help you quickly. The very minimum would have been 'karyoplotr' and 'R'. I have adapted the tags too.
Hi after submitting the question, I realised to add more explanation. I was thinking to add tag such as itself tool name. I have added tags. Thanks for suggestion.
And you removed the code formatting. Why do I even bother to help...
Hello
I didnot remove coding . I really appriciate your suggestions .