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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Add PNG and PDF for compiled Figure S3 #1310

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR adds the compiled Figure S3:

Reviewers: Please confirm this is the right oncoprint plot. What is included here is primary_only, but there is also a figure panel figures/pdfs/supp/figs3/panels/primary_plus_other_supplemental_oncoprint.pdf for primary_plus. The slides version of this figure shows just primary_only, so that's what I compiled here. The current caption stub in the manuscript doesn't clearly spell out if this is meant to be primary only or plus -

Oncoprint of canonical somatic gene mutations, CNVs, fusions, and TMB (top bar plot) for the top 20 genes mutated across rare CNS tumors (N < 5 each): desmoplastic infantile astrocytoma and ganglioglioma (N = 1), germinoma (N = 4), glial-neuronal NOS (N = 4), metastatic secondary tumors (N = 3), neurocytoma (N = 2), and pineoblastoma (N = 3). Patient sex (germline_sex_estimate) and tumor histology (cancer_group) are displayed as annotations at the bottom of each plot. Only samples with mutations in the listed genes are shown. Multiple CNVs are denoted as a complex event.

If the panel figures/pdfs/supp/figs3/panels/primary_plus_other_supplemental_oncoprint.pdf is indeed not going to be used, we should remove it and comment out associated aspects of its generating script.

jharenza commented 2 years ago

Correct, this should be primary only and we are not using primary-plus oncoprints for the manuscript. Can add an additional note to the S3 legend or text.

sjspielman commented 2 years ago

Changes do not affect CI. Merging before checks are complete.