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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Figure S2 H-I are no longer ordered by median TMB #1563

Closed jharenza closed 2 years ago

jharenza commented 2 years ago

TMB plots for S2 H-I became unordered when previously ordered by ascending median TMB, so I think these should be updated :(

Note: I don't think this blocks converting the manuscript to a document for distribution.

sjspielman commented 2 years ago

Since I've worked on them, these plots have never been ordered by median TMB, but instead by frequency of cancer group.

This is set in these lines of code - https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/b6a006d2071bfd41608ec61bc9958432e0427c49/figures/scripts/supp-tmb-compare-panels.R#L148-L156

Based on git history, this script has always produced plots ordered by cancer group frequency - https://github.com/AlexsLemonade/OpenPBTA-analysis/commit/996a0011b60b42772342b16167fa3656a730f110#diff-0e7567890c35e6fcfd9ee4fbdc38355de36ae4c1a4e50c789d0a2284737b6fcd

Edit - (sorry entered too soon) - Either way these plots can be updated to be arranged by median TMB, but this would be a new change, not a reversion.

jaclyn-taroni commented 2 years ago

It's a reversion in a way – just wanted to add some additional context. We used to make TMB panels in this deprecated figure script:

https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/b6a006d2071bfd41608ec61bc9958432e0427c49/figures/scripts/deprecated/mutational-landscape.R#L92-L130

Which uses this function that does order by median:

https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/b6a006d2071bfd41608ec61bc9958432e0427c49/analyses/tmb-compare/util/cdf-plot-function.R#L85-L91

sjspielman commented 2 years ago

I see, thanks for context @jaclyn-taroni!

This should be fairly quick to update either way, so I can start working on it.