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livnatje / DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
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Tutorial Example Issue: Error in beanplot : could not find function "beanplot" #27

Closed 98xy closed 2 years ago

98xy commented 2 years ago

Hi, I tried to test the example and am running into a few issues. When I run this code in the example wiki: R<-DIALOGUE.run(rA = rA,main = "test",k = 2,results.dir = "test", plot.flag = T,conf = "cellQ",pheno = "pathology",n.genes = 100) it returned an error: Error in beanplot(scores ~ treatment * conditions, ll = 0, las = 2, main = main, : could not find function "beanplot" In addition: Warning messages: 1: In file.remove(paste0(results.dir, "DIALOGUE1_", main, ".rds")) : cannot remove file 'testDIALOGUE1_test.rds', reason 'No such file or directory' 2: In file.remove(paste0(results.dir, "DIALOGUE2_", main, ".rds")) : cannot remove file 'testDIALOGUE2_test.rds', reason 'No such file or directory'

Do you have any suggestions? Thank you!

platform x86_64-w64-mingw32 system x86_64, mingw32 version.string R version 4.2.1 (2022-06-23 ucrt)

sangwookbae commented 2 years ago

For me, installing 'beanplot' package using CRAN or BiocManager solved the problem .

BiocManager::install('beanplot')

or

install.packages('beanplot')

Hope it works.

livnatje commented 2 years ago

Thanks for letting us know. We added beanplot as a dependency.