Add UMAP module #29
Add UMAP module #29
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Great PR. Comments I made on plots applied to most of the rest of the plots so please apply to all if you choose.
Major comment for plots is the vertical grid lines on the background are present but the horizontal grid lines are absent. I suggest adding the horizontal grid lines or removing the vertical grid lines.
The scripts were clean and readable. I think after reading comments and deciding what changes you want to make to the plots you are ready to merge.
Not required, but if you want me to take another look at plots after you have made edits I would be happy to do so, just re-request my review!
4.analyze_data/notebooks/UMAP/figures/UMAP_Plate_1_cell_count.png
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4.analyze_data/notebooks/UMAP/figures/UMAP_Plate_1_genotype.png
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@MikeLippincott Thanks so much for the review and addressing my questions in person! I will be merging now. |
Add UMAP module
In this PR, I generate UMAPs for each plate, labeling various metadata, including genotype and cell count. Only for Plate 4 do I include a UMAP labeled for siRNA (shape) and dose (gradient color).
What I need reviewed
Please review everything except for the UMAP TSV files. I would love feedback on how the plots, specific colors, and the code to generate the UMAPs.