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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Update oncoprint figures for V22 #1519

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Closes #1484

This PR updates and re-runs the script figures/scripts/fig2-oncoprint-landscape.R to make oncoplots with V22. The code was specifically updated to include V22 cancer groups such that cancer_group_display column is used for labeling, and cancer_group_hex is used for colors (since the oncoprint_hex column had been removed from palette). In addition, because the oncoprint_include column had also been removed from the palette file, I only filtered on oncoprint_group to identify which cancer groups to include. If this strategy captures too many cancer groups, we may need to incorporate some hard-coding. Finally, I added in a check in the script to error out if the expected scratch/ directory files are present.

jaclyn-taroni commented 2 years ago

@sjspielman this needs another pass with the legend ordering: https://github.com/sjspielman/OpenPBTA-analysis/blob/bd63b4e60bdc85b2b9d74c0c5e39bb784150dfa6/figures/scripts/fig2-oncoprint-landscape.R#L216-L244

The legend order is hard-coded because it is intended to mirror whatever order the cancer groups are in in the figure itself, mostly because it can help a reader if they are having trouble distinguishing between two cancer groups with similar-ish colors. Granted, the comment here (https://github.com/sjspielman/OpenPBTA-analysis/blob/bd63b4e60bdc85b2b9d74c0c5e39bb784150dfa6/figures/scripts/fig2-oncoprint-landscape.R#L212-L214) could definitely be more explicit!

Taking the low-grade oncoprint as an example:

primary_only_lgat_oncoprint

The cancer group order, by my read, is: Pilocytic astrocytoma, Other low-grade glioma, Ganglioglioma, Pleomorphic xanthoastrocytoma, Subependymal Giant Cell Astrocytoma

Taking a look at the legend:

Screen Shot 2022-07-09 at 9 09 07 AM

If we were to put those next to each other as is, I think it'd potentially trip people up.

We should also drop DIPG from the HGAT legend.

I believe the other two legends are all set, but I'd double (triple?) check just to be sure!

sjspielman commented 2 years ago

@jaclyn-taroni definitely missed that legend ordering! I was so excited to get the names right 😂 but you are absolutely correct we need to have the right order. On it!