Add compiled figure S5 - Githubissues

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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Add compiled figure S5 #1313

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR adds compiled PDF and PNG Figure S5.

The exported size of the two scatterplots in this figure was updated for panels to fit in line
A compiled PDF was added as figures/pdfs/supp/figs5/figureS5.pdf
A compiled PNG was added as figures/pngs/figureS5.png

Two questions for reviewers:

The UMAP legend for LGG is labeled colored_subtypes. I think I should update this to match the other legends
We should generally firm up terminology: HGG and LGG, or HGAT and LGAT. I can update legend titles accordingly as needed

jharenza commented 2 years ago

The UMAP legend for LGG is labeled colored_subtypes. I think I should update this to match the other legends

Agree - subtype is probably ideal for all legends

We should generally firm up terminology: HGG and LGG, or HGAT and LGAT. I can update legend titles accordingly as needed

We have been interchanging these, but I suppose since the community knows this better as HGG and LGG, and our subtyping table/histology file uses HGG and LGG, we should stick with these. We can make sure to go through the paper and update as well.

sjspielman commented 2 years ago

This has been updated -

LGG and not LGAT in legend key
Use subtype for all subtype legends, and add code to ensure this legend is second when there are two legends
Tweak of figure sizes to fit in compiled version more cleanly
Compiled PNG/PDF updated with these new plots