Closed jenna-tomkinson closed 7 months ago
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It's a really nice figure! 🎉
Here are a couple nitpicks:
Phenotype Category
should be Phenotype category
, Single Cell Counts
should be Single cell counts
, y axis title as well.) The mitocheck phenotype classes themselves do not need to be changed! (except probably make text a bit bigger)Image Analysis
-> Image analysis
) - use a keen eye for these details!...
) and training data represents in LOIO. 2) It's unclear why there is an arrow that points from LOIO to the JUMP analysis, maybe the JUMP analysis deserves it's own box under the same "generalizability" header? 3) It is unclear why it is important to show with a cartoon that there are 51 plates (it takes up a lot of space). Why not just say JUMP-CP Pilot (51 plates)
> (4) inrease font size in jump umap;A
/ B
) are a bit smallHappy to give this another look after the second iteration!
Here is what I have implemented based on your review:
Dark2
palette from RColorBrewer. I think it clashes less, but please let me know if this should be changed as well. Here is also the link to the different palettes if you see one that would be better: https://r-graph-gallery.com/38-rcolorbrewers-palettes.html. Made the tags much bigger and fixed the alignment issue/whitespace issue by making the plot "free" per the documentation to avoid patchwork from trying to align itself.
I look forward to more improvements after your next review!
More nitpicks:
Extract nuclei features (257)
(I don't remember if this is the actual number or not, I just took a guess!)Figure 1: Class counts and workflow
@gwaybio Thank you lots for the review! This was a great first exercise with patchwork and I am excited to work more on creating figures! I will be merging now after addressing your comments, but please feel free to let me know if anything else needs to be updated.
Add Figure 1
In this PR, figure 1 for the manuscript has been created in R using patchwork. Panel A is generated in the notebook, and Panel B is created in BioRender and saved as PNG.