Add new MAGIC API #195
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Add new MAGIC API #195
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Makes sense! 😄 |
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Fix #187 and #193
The bulk of the new API is contained within https://github.com/KrishnaswamyLab/MAGIC and https://github.com/KrishnaswamyLab/graphtools , both of which now natively accept AnnData as of KrishnaswamyLab/MAGIC#116 and KrishnaswamyLab/graphtools#18. MAGIC also returns an AnnData object containing the original
.obsand (optionally subsetted).varfrom the input. ThescanpyAPI forces this to be a newAnnDataif the genes are subsetted, allows modification in-place if all genes are returned, and adds the returned values to.obsm['X_magic']if the returned values are PCA on MAGIC.@falexwolf let me know if this fits what you think the API should be.