Pipeline Flowchart - Editing Pixie Pipeline Section #869
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Let's try and merge this into #856 if possible, since my PR will be addressing general cleanup requests from Candace. |
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alex-l-kong
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Dec 19, 2022
* Remove extraneous pixel_cluster_prefix arg from create_pixel_matrix * Remove cell_cluster_prefix from notebook * Make norm_vals_name naming convention consistent with channel_norm prefix * Change channel_norm.feather format to match channel_norm_post_rowsum.feather * Rename pixel_norm to pixel_thresh * Specify weights as SOM weights and remove saving of SOM to meta cluster mapping * Clarify cell_counts_norm as size normalized in naming conventions * Save weighted_cell_channel_name as a feather file instead of csv * Remove extraneous 's' at the end of meta_cluster_count_avgs files * Rename clustering notebooks to ensure they're identified as Pixie * Rename notebooks to use up-to-date names * PYCODESTYLE * Ensure 'size_norm_name' propagates into notebook * weights_name to cell_weights_name change in notebook * Notebook variable adjustments * Make sure example dataset doesn't have any unnecessary prefixes in it * Ensure cluster_counts_norm_name passed wherever necessary * Cell clustering documentation fixes * Write out cluster counts size norm instead of cell mat for cell cluster notebook test * Don't write out extraneous cell_mat.feather * Ensure tests match up with updated sans-cell_mat process (we really need to refactor to OOP...) * Patch up test_utils dimensions for _make_neighborhood_matri * Initial pass at reorganizing files * Remove extraneous print statements * Reorganize pixie notebooks so example data download is the first thing; renumber pixel clustering notebook * Ensure example dataset pulls from the correct HuggingFace hash * Final documentation changes addressed * Reorganize all notebooks so example dataset download is at the beginning * Update file names in README.md to reflect updated names in notebooks * Fix another instance of example_pixel_clustering.ipynb * Fix more incorrect notebook name paths * Ton of notebook reorganization * Fix an instance of example_cell_clustering * Fix missing comma in example_neighborhood_analysis_script.ipynb * updated pipeline flowchart (#869) * Update revision to main for example dataset * Change a couple of cell output prefixes to match HuggingFace outputs Co-authored-by: Sricharan Reddy Varra <srivarra@stanford.edu>
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What is the purpose of this PR?
Closes #868.
How did you implement your changes
Added
Pixiename in Notebooks 2 and 3 in the Pixie Pipeline section of the flowchart.Remaining issues
N/A.