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asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
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upset R package compatibility #18

Open chrisamiller opened 5 years ago

chrisamiller commented 5 years ago

In the R upset package installed in the bioconda/quay repository, the options mainbar.y.label and sets.x.label do not exist, causing a failure:

$ intervene upset --names A,B,C -o . -i $a $b $c

Running UpSet module. Please wait...

Error in upset(fromExpression(expressionInput), nsets = 3, nintersects = 30,  :
  unused arguments (mainbar.y.label = "No. of Intersections", sets.x.label = "Set size")
Execution halted

You are done! Please check your results @ ..
Thank you for using Intervene!

This removes those options, which allows it to proceed

asntech commented 4 years ago

Hello @chrisamiller! Please accept my apologies for getting back to you very late. Do you remember what version of R and UpSet package you were using? Thanks!

chrisamiller commented 4 years ago

I don't know offhand, but I was running it from the bioconda container, so the environment should be available in that docker image: https://bioconda.github.io/recipes/intervene/README.html

Thanks for looking into it!

asntech commented 3 years ago

This seems to be due to the older version of UpSetR. Please check https://github.com/asntech/intervene/issues/38