Setting Altered Changes Annotation Colour Order

[DarioS]

Changing nothing else apart from the value of altered, the clinical data colouring swaps labels (for WGD but not for the second variable).

This seems unintended.

[PoisonAlien]

Hello, Sorry for the delay in getting back. Can you post your command? Does it happen when you manually provide colours for annotations?

[DarioS]

I could not trigger it using a minimal example, so you'll need to load the attached R objects testData.zip The command is

load("testData.RData") # After unzipping.
oncoplot(MAF, colors = customColours, top = 50, showTumorSampleBarcodes = TRUE, removeNonMutated = FALSE,
         clinicalFeatures = c("WGD", "TP53_LOH"), sortByAnnotation = TRUE, sortByMutation = TRUE,
         annotationOrder = c("No", "Yes"), genesToIgnore = "TTN",
         gene_mar = 6, barcode_mar = 11)

Just add altered = TRUE to get the swapping of WGD legend.

[PoisonAlien]

Thanks for the data. I can reproduce it. I will take a look into it soon. Meanwhile you can use annotationColor argument to define color codes which should maintain the correct color order.

oncoplot(
  MAF,
  colors = customColours,
  top = 50,
  showTumorSampleBarcodes = TRUE,
  removeNonMutated = FALSE,
  clinicalFeatures = c("WGD", "TP53_LOH"),
  sortByAnnotation = TRUE,
  sortByMutation = TRUE,
  annotationOrder = c("No", "Yes"),
  genesToIgnore = "TTN",
  gene_mar = 6,
  barcode_mar = 11,
  altered = TRUE,
  annotationColor = list(
    WGD = c("Yes" = "red", "No" = "blue"),
    TP53_LOH = c("Yes" = "red", "No" = "blue")
  )
)

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[DarioS]

Swapping still happens in the latest release of maftools.

[PoisonAlien]

Hi, I'm on holidays. I'll fix them the next week.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[DarioS]

Stale but important.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.