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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Error in g$grobs[[legend]]: no such index at level 2, when calling peaks #2168

Open nansne opened 3 months ago

nansne commented 3 months ago

I encountered this error during call peaking, while the call peaking process has been completed. However, I got an error message that says "Error in g$grobs[[legend]]: no such index at level 2". and ggplot2 had been installed. image Has anyone encountered this situation before? Please advise,Thank you very much

rcorces commented 3 months ago

Hi @nansne! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

KaiLi-2324 commented 3 months ago

Hi, @nansne Did you solve the problem? I encountered the same error.

lzj1769 commented 1 month ago

This is related to the plotting function called by addReproduciblePeakSet

You can set plot = FALSE to avoid this error.

proj <- addReproduciblePeakSet(
    ArchRProj = proj, 
    groupBy = "Sample", 
    cutOff = 0.01,
    pathToMacs2 = pathToMacs2,
    plot = FALSE
)

At least, this worked for me.

zqfang commented 1 week ago

I had the same issue with addDoubletScores, but after installing ggplot2 v3.4.2, it worked for me.