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I am getting errors with anything related to ggplot. I have done as suggested in previous thread by reinstalling Cairo, Quartz and ggrastr, however this has not fixed the problem. The issue is observed firstly, in Arrow file generation:
Continuing through after error ggplot for TSS by Frags
And then again during doublet scoring ggplot generation:
RROR Found in ggplot for Untreated (4 of 5) :
LogFile = ArchRLogs/ArchR-addDoubletScores...
<simpleError in g$grobs[[legend]]: no such index at level 2
>
In each case pdf files are generated for the specific plot hone when I try and access them I am met with an error message that the file is broken or damaged as shown below ( also tried opening is two different pdf viewers and was met with similar issues) :
Hi @shamer3! 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.
Hi Julia, thanks so much I can confirm downgrading to ggplot 3.3.0 has solved the plotting issue. Something with ggplot 3.5.0 is bugging all the plots out. Thanks!!
I am getting errors with anything related to ggplot. I have done as suggested in previous thread by reinstalling Cairo, Quartz and ggrastr, however this has not fixed the problem. The issue is observed firstly, in Arrow file generation:
And then again during doublet scoring ggplot generation:
In each case pdf files are generated for the specific plot hone when I try and access them I am met with an error message that the file is broken or damaged as shown below ( also tried opening is two different pdf viewers and was met with similar issues) :
Session information is as follows:
The text was updated successfully, but these errors were encountered: