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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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runSCENIC_3_scoreCells errors: Error in plot.new() and Error in .Call.graphics(C_gridDirty) #165

Open pgugger opened 3 years ago

pgugger commented 3 years ago

Hi, When running scenicOptions <- runSCENIC_3_scoreCells(scenicOptions, exprMat) on my own data set, I get two errors:

Error in plot.new() : figure margins too large
Error in .Call.graphics(C_gridDirty) : invalid graphics state

exprMat is 21259 by 142 and represents only a small number of cells from our total dataset that we ultimately hope to analyze.

I am running SCENIC on MacOS in the terminal with R 4.0.2 and the latest versions of all the packages. I tried wrapping the command in pdf() ... dev.off() with a large height and width but that didn't help. Any suggestions?

Thank you for your help.

Meggie-MH commented 2 years ago

Do you find a way to fix the error? If so, would you mind sharing? Thank you.

pgugger commented 2 years ago

If I recall correctly, I did not find a solution to this. So, I abandoned the R version (possibly there were other errors I don't recall) and used the Python one, then loaded the results tables back into R (thad to manually edit some headers first). I had a lot of trouble with the Python one too, though. I suspect some of these kinks may have been worked out since, but I have not tried more recently.

yamihn commented 8 months ago

Hi, did someone find a solution here?

Sogand65 commented 4 months ago

Hi, I have the same issue, does someone have a thought on this?

Thanks