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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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PrettyOncoplot example in vignette throws an error #78

Closed rdmorin closed 2 years ago

rdmorin commented 2 years ago

This section of the vignette throws an error that I believe has a known fix involving specifying a NULL value for one argument. Can we fix this function to handle this error more elegantly and update the vignette? I suspect the issue is due to the new MAFs no longer having the noncoding mutations in them. 

prettyOncoplot(maftools_obj = maf,
               genes = genes,
               these_samples_metadata = all_meta,
               metadataColumns = c("pathology", "lymphgen", "sex", "EBV_status_inf", "cohort"),
               sortByColumns = c("pathology", "sex", "lymphgen", "EBV_status_inf", "cohort"),
               keepGeneOrder = TRUE,
               splitGeneGroups = gene_groups,
               splitColumnName = "pathology",
               metadataBarHeight = 5,
               metadataBarFontsize = 8,
               fontSizeGene = 11,
               recycleOncomatrix = TRUE,
               removeNonMutated = FALSE)
NFKBIZ and 3'UTR
HNRNPH1 and Splice_Region
Error in if (mat[gene, samp] == "") { : 
  missing value where TRUE/FALSE needed
rdmorin commented 2 years ago

adding include_noncoding = NULL usually works but there's another error thrown:

Error: pathology: cannot map colors to some of the levels: BLL
mattssca commented 2 years ago

Addressed in this PR