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upset R package compatibility #18

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upset R package compatibility #18

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chrisamiller
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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

@chrisamiller
rm sets.x.label and mainbar.y.label from R code
e96beec 
These two params don't exist in the upset R package version that's packaged with intervene in Conda. Removing this fixes the problem.
@chrisamiller
remove mblabel and xlabel options
a0ae7e2 
they don't exist in the R package
@chrisamiller
Merge pull request #1 from chrisamiller/patch-1
0125f31 
rm sets.x.label and mainbar.y.label from R code
@asntech
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asntech commented Oct 19, 2019

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
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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
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asntech commented Oct 14, 2020

This seems to be due to the older version of UpSetR. Please check #38

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@chrisamiller @asntech