fix t-SNE in plot_representation and Add UMAP support - #14
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alihamraoui wants to merge 2 commits into
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Do we really want to support both? I think everyone uses UMAP now, what do you think @HakimBenkirane? If we use the UMAP only, we can simply update the docstrings to mention "UMAP" instead of "t-sne"! |
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Yes, UMAP is the default we can just change the docstrings |
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plot_representationdocumentation says it runs t-SNE, but it actually runs UMAP.plot_representationnow supports both t-SNE and UMAP via amethodargument.t-SNE now defaults to
learning_rate='auto', which fixes collapsed single-blob layouts on small datasets caused by scanpy's legacy fixed learning rate.