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Especially when we visualize raw counts, sometimes it's hard to see the differences between DEGs and other genes in the heatmap since one value can simply dominate the entire heatmap. I think we can add a scaling option to matrixplot, which squashes expression values between 0 and 1 to make markers more pronounced.
Allow greater customizability and visibility when using dotplot by allowing the user to set the smallest dot size.
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@falexwolf I updated the visualizations example notebook to reflect the changes: scverse/scanpy_usage#11 |
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Thank you! Shall we close @gokceneraslan PR then? Or do we need to merge it first and then merge this? Thanks for clarifying! Regarding the examples: it's a bit unfortunate, but we migrated to https://github.com/theislab/scanpy-tutorials, and |
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I think this PR has all the commits from two other PRs. Tricky to set up 😛 We can close mine. |
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Cool! I'll merge this then. Thanks everybody! |
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@falexwolf Thanks. I will add the PR to scanpy-tutorials |
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standard_scale to plots
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This PR extends the original PR #512 by @gokceneraslan which adds the
standard_scalingparameter to matrixplot.I added the same functionality to dotplot, heatmap and stacked_violin.
Also, I integrated PR #524 by @sjfleming which adds a
smallest_dotoption to dotplot.