Step 4 refactoring + Scanpy updates

genepattern / single_cell_clustering_notebook

BSD 3-Clause "New" or "Revised" License

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Step 4 refactoring + Scanpy updates #18

Closed alex-wenzel closed 5 years ago

alex-wenzel commented 5 years ago

The majority of these commits are for refactoring the "Step 4" figures into multiple sub-steps. Also miscellaneous duplicate code deletion and documentation changes, and makes the notebook compatible with the GenePattern Notebook Python 3.7 environment with Scanpy 1.3.4. It is worth noting that this pull request also makes the notebook incompatible with the Python 3.6 GenePattern Notebook environment due to its significantly older version of Scanpy.

alex-wenzel commented 5 years ago

Also removed the "save plot" buttons as they appear to be broken in GenePattern notebooks at the moment and users can save most plots with Plotly functionality as well.