short_histology "Other" groups disparate types

[jashapiro]

What data file(s) does this issue pertain to?

pbta-histologies.tsv

What release are you using?

v15

Put your question or report your issue here.

The short_histology label as it currently is used contains a category called "Other", which includes tumor histologies of vastly different types, which can lead to improper grouping if it is used as the main label for a figure or analysis. For example, it includes "Benign tumors" (as labeled in broad_histology) such as Fibromas and Dermoid Cysts, but also "Metastatic secondary tumors", which I would imagine we would almost never want to group together.

We may want multiple "Other" categories, such as "Other-benign"?

I do not know if this may be resolved as part of #637, but any resolution will almost certainly result in breaking changes, not least for the color palettes in #622.

(tagging in @allisonheath for coordination)

[jharenza]

cc-ing @baileyckelly and @allisonheath to weigh in on this! As I am looking over the figures, I am thinking perhaps instead of Other, we may want to add short_histology for these tumors. I think these were all Other in the KidsFirst database, but I added the actual diagnoses from our CBTTC database. Maybe this is something @baileyckelly already has solved, though!

[jharenza]

@jashapiro based on internal discussion, we will not update this for #732 but will discuss for a future release.

[sjspielman]

Noting that since this issue was opened, cancer groupings are primarily used:

• This module introduces the cancer_group grouping
• Groupings used in the manuscript are completed and described here where their respective color palettes are created.