angelolab / ark-analysis / 3565
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Add cell clustering steps in (#420)

* Initial setup of train_cell_som

* Add initial cell clustering results

* Forgot to update tests with new function names

* More function fixes

* PYCODESTYLE

* Fix documentation of cell_consensus_cluster

* Another docstring fix

* Add parameters to set learning rate and normalize in run_cell_som.R

* Remove unnecessary subset

* Fix 99.9% normalization in run_cell_som.R

* Typo

* Add row sum normalization and removal of zero sum rows to R script files

* Confirm cell clustering

* Make comments clearer

* Remove redundant fov from fov_pixel_data

* Fix parameters in example_flowsom_clustering.ipynb

* Remove subtracting by 1 error

* Clarify comments for cell clustering

* Almost all code review comments addressed

* Add efficiencies to pixel clustering and cell table merging

* Fix comments and print outs

* PYCODESTYLE

* Tests, lot's of tests...

* Add check to verify_same_elements that tests for order, and make sure ordering is ensured before run_pixel_som and run_cell_som

* Fix col_index -> column_index

* More index fixing

* Index fixes for clustering cells

* Add updated FlowSOM notebook with results

* Add metadata for cluster_cells test

* Move row sum normalization to Python, keep column percentile normalization in R

* Update FlowSOM notebook, and update notebook tests (hold off on cell clustering tests until we see what Brian discovers about Travis testing with R)

* Update error message printed by verify_same_elements if enforce_order=True

* PYCODESTYLE

1440 of 1510 relevant lines covered (95.36%)

0.95 hits per line

Jobs
ID Job ID Ran Files Coverage
1 3565.1 (MPLBACKEND=Agg) 0
95.36
 Travis Job 3565.1
Source Files on build 3565
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