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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Figure S1 as PNG and PDF #1304

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR adds the compiled Figure S1 as both PDF and PNG. (This figure is a single panel, so there is not much actual "compilation.")

Reviewers: Please check if these files are in the expected place and have the expected name. We may also want to update figures/README.md to clearly state naming scheme for these panels, which can be added in this PR during review.

jaclyn-taroni commented 2 years ago

We need PNG for things to render in the Manubot version and PDF for submission. Putting compiled figures in figures/pngs and figures/pdfs is documented in figures/README.md. If we're going to do a reorganization, it's probably best to do it in the end after we've finished the compiled figures.

jharenza commented 2 years ago

We need PNG for things to render in the Manubot version and PDF for submission. Putting compiled figures in figures/pngs and figures/pdfs is documented in figures/README.md. If we're going to do a reorganization, it's probably best to do it in the end after we've finished the compiled figures.

oh gotcha, this is because it is the full figure! So then, should Figure_S1.png go in figures/pngs/ with a new folder called supp, etc and the current PNGs in that folder be deleted and folders added per figure such as with the pdf directory? having one in a folder but one not was what threw me off.

jaclyn-taroni commented 2 years ago

These additions are in different places than I would expect. I would expect:

figures/pdfs/supp/figs1/Figure_S1.png -> figures/pngs/figureS1.png figures/pdfs/supp/figs1/panels/Figure_S1.pdf -> figures/pdfs/supp/figs1/figureS1.pdf

The file name style (i.e., Figure_S1.* vs. figureS1.*) is not well-defined in the docs, but this is closer to what I have in #1305 🤷🏻

sjspielman commented 2 years ago

These additions are in different places than I would expect

Ah, I see I misread something in the README! Will update.

sjspielman commented 2 years ago

@jaclyn-taroni this has been updated. I also made a small change to the README about convention for supplementary compiled PDFs.

jaclyn-taroni commented 2 years ago

Addition of non-programmatically generated figure and docs, merging without CI