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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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V22 Compiled Figure 2 #1530

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1485 This PR adds compiled versions of Figure 2 (oncoprint), both PDF and PNG. For this one, I ended up switching the order of the alteration and sex legends, so now the alterations are on top. I think this is more consistent with plots where sex is annotated below the oncoplot.

jharenza commented 2 years ago

Hi @sjspielman! Thanks for adding this.

Can you add a title to the legends for "Germline sex estimate" or "Sex" and "Alteration"?

I also just noticed, and did not catch this in the old compiled figures, that we do not have the row annotation labels for "Sex" and "Cancer group". Can we add these? We only have two annotation rows and people can probably assume what's what there, but I think it should be clearly labeled on the oncoprint.

sjspielman commented 2 years ago

Sure, I can add those back in. I actually agree with you here. I can't track it down now, but previous conversations at some point (can't remember exact details) had led to those being removed. I'll relabel!

jharenza commented 2 years ago

I wonder if it was because they had underscores- I recall we couldn't remove them in the plot. Maybe the intention was to label during compilation? 🤷🏻‍♀️

sjspielman commented 2 years ago

@jharenza I added back in legend titles.

sjspielman commented 2 years ago

This PR does not modify code so does not need to run through CI.