angelolab / ark-analysis / 4594

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Add more descriptive visualizations for pixel and cell clustering (#460)

* Visualizations 1-4 in progress

* Fix docstring

* Fix a few tests

* Typo in docstring

* Docstring fix

* Docfix in right location

* Visualizations 5-6 added in

* Adjust tests to account for cell_size normalization

* Visualizations 7-8 done

* Docstring fix in compute_cell_cluster_counts

* Version commit of cell clustering

* Address a lot of Candace requests

* Update pipeline to include weighted cell channel expression heatmaps

* Notebook documentation link sweetener

* Initial addressing of code review comments

* More code review comments addressed

* Remove comments

* Update notebooks to include changes made in addressing code review comments

* Remove stray line in data_utils.py that clipped all segmentation label 1's from Candace's dataset

* Remove viz arguments to former viz functions that now just return the data

* Convert visualization into pure computational functions and add more testing

* Update cell clustering notebook to separate computation from visualization

* Update pixel clustering notebook

* Update cell clustering notebook

* Address a TON of code review comments

* Docstring

* Add img_sub_folder argument to create_pixel_matrix

* Suffix fix in data_utils

* Add img_sub_folder argument into example_pixel_clustering

* Replace cluster_prefix with None

* Initial work on .csv saving (likely to be retconned)

* Address final code review comment (saving to CSV)

* Doc fix

* Add new notebooks

* Clarify comment in cell clustering notebook

* Add FINAL final correction (normalize by cell size prior to running R)

* Update notebook documentation: saving to .csv, not .feather

* First Candace comments addressed (everything not in the notebook, and NOTE in pixel clustering

* Doc fix

* Add prefixes to all variables in the notebooks

* Address a hella ton of code review co... (continued)

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