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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Figure S2 panels #1279

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR addresses Issue #1254 and creates several panels for Figure S2:

Panel File Generating script
A figures/pdfs/supp/figs2/panels/pbta_vaf_cor_matrix.tiff supp-snv-callers-panels.R
B figures/pdfs/supp/figs2/panels/pbta_vaf_distribution_plot.pdf supp-snv-callers-panels.R
C figures/pdfs/supp/figs2/panels/pbta_upset_plot.pdf supp-snv-callers-panels.R
D figures/pdfs/supp/figs2/panels/tcga_vaf_cor_matrix.pdf supp-snv-callers-panels.R
E figures/pdfs/supp/figs2/panels/tcga_vaf_distribution_plot.pdf supp-snv-callers-panels.R
F figures/pdfs/supp/figs2/panels/tcga_upset_plot.pdf supp-snv-callers-panels.R
G figures/pdfs/supp/figs2/panels/lancet_wxs_wgs_plot.pdf supp-snv-callers-panels.R
H figures/pdfs/supp/figs2/panels/pbta_tmb_cdf_plot.pdf supp-tmb-compare-panels.R
I figures/pdfs/supp/figs2/panels/tcga_tmb_cdf_plot.pdf supp-tmb-compare-panels.R

Places for reviewers to look:

Documentation Checklist

jaclyn-taroni commented 2 years ago

@sjspielman something is wrong with the upset plots here

jaclyn-taroni commented 2 years ago

The panel figures/pdfs/supp/figs2/panels/tcga_tmb_cdf_plot.pdf uses Okabe Ito colors. Look ok?

The colors here are a little bit into chartjunk territory IMO. As far as I know, these diagnoses don't come up anywhere else in the manuscript and they're already a grouped plot.

sjspielman commented 2 years ago

The colors here are a little bit into chartjunk territory IMO. As far as I know, these diagnoses don't come up anywhere else in the manuscript and they're already a grouped plot.

I added them to be "consistent" with the PBTA panel next door which does have colors. Can make these all gray in TGCA; also PBTA though?

sjspielman commented 2 years ago

something is wrong with the upset plots here

This is super odd, they open on my computer. I'll try re-adding them..? Edit: something is indeed super odd because they only sometimes open. Investigating.

jaclyn-taroni commented 2 years ago

I added them to be "consistent" with the PBTA panel next door which does have colors. Can make these all gray in TGCA; also PBTA though?

Right, but the PBTA panel has colors for a very specific reason: a reader should be able to identify a cancer group (display) across figures.

sjspielman commented 2 years ago

Upset plots have been recovered, and TCGA cdf plot points are now all gray

jharenza commented 2 years ago

@sjspielman I went ahead and dropped the figures in the google slideshow and it looks like lancet_wxs_wgs_plot.pdf and tcga_tmb_cdf_plot.pdf could benefit from a smaller width to fit. If it helps, you can add the CDF panels together like before, so the x-axis widths are similar sizing, and we can add the panel letters later.

sjspielman commented 2 years ago

@jharenza thanks! I updated plot dimensions so hopefully they'll fit better now. Do these sizes work?

sjspielman commented 2 years ago

@jharenza I'm going to merge this in so we can more towards solidifying the overall generate_figures.sh script, and as needed should be quick to change figure sizes for paneling in another PR!