Error in `prettyOncoplot`

[vladimirsouza]

maf_metadata <- get_gambl_metadata(seq_type_filter = "genome") %>%
  dplyr::filter(pathology %in% c("FL", "DLBCL"))

maf_data <- get_ssm_by_samples(
  these_samples_metadata = maf_metadata
)

fl_genes = c("RRAGC", "CREBBP", "VMA21", "ATP6V1B2")

dlbcl_genes = c("EZH2", "KMT2D", "MEF2B", "CD79B", "MYD88", "TP53")

genes = c(fl_genes, dlbcl_genes)

gene_groups = c(rep("FL", length(fl_genes)), rep("DLBCL", length(dlbcl_genes)))
names(gene_groups) = genes

prettyOncoplot(
  maf_df = maf_data,
  genes = genes,
  these_samples_metadata = maf_metadata %>%
    arrange(patient_id),
  splitGeneGroups = gene_groups,
  keepGeneOrder = TRUE,
  splitColumnName = "pathology",
  metadataBarHeight = 5,
  metadataBarFontsize = 8,
  legend_row = 2,
  fontSizeGene = 11,
  metadataColumns = c("pathology", "lymphgen", "sex"),
  sortByColumns = c("pathology", "lymphgen", "sex")
)

All mutation types: Missense_Mutation, Multi_Hit, Frame_Shift_Del, Splice_Site,
Nonsense_Mutation, Frame_Shift_Ins, In_Frame_Del, Translation_Start_Site.
`alter_fun` is assumed vectorizable. If it does not generate correct plot, please set
`alter_fun_is_vectorized = FALSE` in `oncoPrint()`.
Error: elements in `col` should be named vectors.

The error happens in the ComplexHeatmap::oncoPrint call. Here is the object that is given to the col parameter of oncoPrint:

> col
     Nonsense_Mutation      Missense_Mutation              Multi_Hit        Frame_Shift_Ins 
             "#c41230"              "#39b54b"              "#455564"              "#e90c8b" 
       Frame_Shift_Del           In_Frame_Ins           In_Frame_Del       Nonstop_Mutation 
             "#e90c8b"              "#5f3a17"              "#5f3a17"              "#2cace3" 
Translation_Start_Site            Splice_Site          Splice_Region                  3'UTR 
             "#8781bd"              "#fe9003"              "#fe9003"              "#f9bd1f" 
                Silent 
             "#A020F0" 

[Kdreval]

This is duplication of #42