Kmeans notebook minor fixes #966
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What is the purpose of this PR?
Closes #963 and closes #964.
How did you implement your changes
Passed the
cell_type_colarg into the appropriate functions, renamed the arg increate_neighborhood_matrixfrom cluster_name_col --> cell_type_col for consistency.Edited
visualize.draw_heatmapto save images without cropping, and heatmaps are saved by default now.Previously, the output files were saved with the same name each time the notebook was run, unless you manually changed them to indicate counts vs freq or a different cell column. Now, the results are saved to a subfolder within the
neighborhood_analysisdirectory, indicated by the parameters specified by the user (i.e.cell_meta_cluster_radius50_counts)The produced cell table updated with kmeans clusters now saves in this new subfolder, rather than
segmentation/cell_table.Remaining issues
NA