search

bzhanglab / WebGestaltR

R package for WebGestalt
https://bzhanglab.github.io/WebGestaltR/
34 stars 14 forks source link

Execuation halts with error message: Error in plot.new() : figure margins too large #25

Closed Pchaskar closed 1 year ago

Pchaskar commented 1 year ago

Error in plot.new() : figure margins too large Calls: WebGestaltR ... plotEnrichmentPlot -> plot -> plot.default -> plot.new

yxngl commented 1 year ago

Can you try using plotFormat="svg"? Or isOutput=FALSE if you just need the result data frame?

On Mon, May 22, 2023 at 7:29 AM Prasad Chaskar @.***> wrote:

Error in plot.new() : figure margins too large Calls: WebGestaltR ... plotEnrichmentPlot -> plot -> plot.default -> plot.new

— Reply to this email directly, view it on GitHub https://github.com/bzhanglab/WebGestaltR/issues/25, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAM6IVK5QD2FFN5F6AWBFCTXHNL23ANCNFSM6AAAAAAYKL4YCU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

iblacksand commented 1 year ago

I also have seen this occur on the website, but when I reran the same analysis with no changes, the error message didn't appear. This was with GSEA with a list that was sensitive to the random walk and would change results, so I am guessing the error depends on the amount of enriched pathways/drugs/etc. This could probably be fixed by manually setting the margins.

Pchaskar commented 1 year ago

Thanks,

`gseaplotFormat="svg, solved the problem for me.

But I agree this issue occurs occasionally, and re-running resolves it.