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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Compiled figure 5 #1330

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

Partially addresses issues #1321 and #1322 by updating Figure 5 panels and adding the compiled PDF and PNG.

This PR copies the updated Figure 5 panels into figures, adds a line in generate_figures.sh to perform the copying, and adds compiled Figure 5.

One question: should we retain the broad_histology label on the GSVA heatmap?

jharenza commented 2 years ago

One question: should we retain the broad_histology label on the GSVA heatmap?

We did this to match UMAP, but I did find it harder to write about in the manuscript. However, the analysis is also done on broad histology. I think we can either retain broad histology labels and analysis, and add another annotation row for cancer group OR retain broad labels, run another analysis on cancer group and add the annotation for cancer group. I'll just have to update the text for the latter making sure the cancer groups' scores are significant, but it may be useful/easier to write to have the latter results and both labels (that'll require another legend).

sjspielman commented 2 years ago

This PR is now out of date given #1336. I'm going to convert this to a draft and block with the 5D panel.

Edit: Also blocking with #1337 which will update the GSVA analysis and figure use to cancer groups instead of broad histologies.

sjspielman commented 2 years ago

Noting the GSVA panel has been updated with cancer groups. But, this is now blocked by #1347. The figure will need to be recompiled once that is in.

sjspielman commented 2 years ago

@jharenza at long last this is ready again!

Note that as part of this I had to update the overall sizing for the quantiseq panel.

sjspielman commented 2 years ago

The immune-deconv module of interest has passed CI so this can be merged in now.