Update cascade plots

[komalsrathi]

I have made the following changes:

1) Cascade Plots (All genes)

• removed underscore in annotations and legend
• removed CNS region from annotation and legend
• Update Cancer Group with PXA where Molecular Subtype == "PXA"
• replace NA values with "Flag" in Molecular Subtype and Cancer Group
• Update Cancer Group names to the following: DHG -> (DHG) Diffuse Hemispheric Glioma DMG -> (DMG) Diffuse Midline Glioma HGG -> (HGG) High Grade Glioma (not otherwise specified) IHG -> (IHG) Infantile High Grade Glioma PXA -> (PXA) Pleomorphic Xanthoastrocytoma

2) Cascade Plots (Top 20 genes)

• removed underscore in annotations and legend
• removed CNS region and Molecular Subtype from annotation and legend
• Update Cancer Group with PXA where Molecular Subtype == "PXA"
• replace NA values with "Flag" in Molecular Subtype and Cancer Group
• Update Cancer Group names to the following: DHG -> (DHG) Diffuse Hemispheric Glioma DMG -> (DMG) Diffuse Midline Glioma HGG -> (HGG) High Grade Glioma (not otherwise specified) IHG -> (IHG) Infantile High Grade Glioma PXA -> (PXA) Pleomorphic Xanthoastrocytoma

Fixes: #89 #90

[mkoptyra]

@jharenza would you be able to help with this review too?

[komalsrathi]

For TMB, I noticed the scale is 0-20. Assuming units are Mut/Mb. Might want to add units. Is it correct that 20 is max? Are any samples ultra-hypermutant, or not in this cohort? An alternative (and can be addressed in another PR) would be to assign the samples as TMB == Normal (<10 Mut/Mb), Hypermutant >=10 but <100, Ultra-hypermutant >=100).

yes 20.65 is max. Yes, units are Mut/Mb.

[komalsrathi]

Can discuss your comment in the upcoming meeting.