Add heatmap visualizations in for SOM results #410
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ngreenwald
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Mar 13, 2021
ngreenwald
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Mar 13, 2021
ngreenwald
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Apr 8, 2021
ngreenwald
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Apr 9, 2021
ngreenwald
requested changes
Apr 9, 2021
ngreenwald
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Mar 9, 2022
* Initial commit of new SOM branch * R SOM integration (#375) * Initial commit of new cluster boost step * Add RST files * Try explicitly downloading cytolib * Try directly installing cytolib * See if changes to cytolib library made it in * Keep only the TIFs we absolutely need for testing * Remove old preprocessing.py and cluster.py files: everything now in som_utils.py and som_runner.R * Decrease size of FlowSOM images to speed up testing * Reduced size of images for segmentation testing too, and adjusted function arguments accordingly * Update to testing: only unit test example_flowsom_clustering.ipynb, and mock up create_pixels instead of directly running it * Add new testing framework * Change the directory structure of the channel data and the segmentation labels, which also requires tests to be updated * Fix a typo in segmentation_dir for testing example_flowsom_clustering.ipynb * Change path in som_utils.py * Remove comments * Adjust path name parameter passing for cluster_pixels and som_runner.R * Add coverage by checking path names in cluster_pixels * Basic path modifications * Add framework for subsetting SOM (#379) * Initial commit of new subsetting strategy * Finalize subsetting method * Fix notebook testing for subsetted som * Add a ton of testing * Nuke references to point * Add tables library to fix import errors, and fix PYCODESTYLE * Remove MIBItiff tests for flowsom clustering and mock up cluster_pixels in notebook test to write to HDF5 file * PYCODESTYLE * Reorganize SOM * Remove old functions and adjust notebook tests for new structure * Correct typo * Add next version of SOM * Need to add feather to autodoc * Documentation fix for cluster_pixels * Documentation fix for train_som * Add seed and num_passes default arguments * Remove extraneous comments * Address code review comments outside of the normalization * Fix indentation in conf.py * Address code review comments * Nuke another h5py * Add consensus clustering process (#394) * Initial commit of consensus clustering * Update notebooks testing to include dummy consensus cluster results creation * Address code review comments * Add 99.9% normalization using subsetted data to run_trained_som.R (#396) * Batch the FlowSOM process (#399) * Batch preprocessing step * Adjust notebook to handle new preprocessing * Add implementation with multiple fovs batched in run_trained_som.R * Remove old cluster batching code * Batch segmentation label loading * Change segmentation labels loading to numpy * Remove old commented code, change create_fov_pixel_mat to return matrices and create_pixel_matrix to save matrices * Fix consensus clustering so it assigns hclust values to each pixel (#407) * Fix hierarchical clustering to assign to every element * Add testing for new consensus clustering method * Remove extra comma * Add heatmap visualizations in for SOM results (#410) * Initial results for visualizing the SOM heatmap * Adjust tests to account for new directory setting in example_flowsom_clustering * Add random seeds * Add seed call to ConsensusClusterPlus * Add numPasses back * Remove channels argument from create_pixel_matrix * Add save directories based on datetime to separate runs * Address code review comments (part 1) * Add numeric random seed * Code review comments part 1 (no directory structure fix yet) * Add new directory setup and notebook testing * Fix typo * Fix directory creation bugs in notebook tests * Change cell ordering * Add metadata columns to SOM cluster and consensus cluster data (#418) * Add Candace's suggestions * Update tests to reflect new method of creating and reading .feathers * Change cluster assignment step from cbind to $ for minor speedup * Fix notebooks_test * Add _feature_1 generation * Re-add notebook tests * 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 * Remove _norm from file paths * Add more descriptive notes to the pixel/cell clustering notebook (#428) * Add descriptive notes to the FlowSOM notebook, add more argument setting parameters, and update notebook tests accordingly * Fix call to execute in notebooks_test_utils * Rename example_flowsom_clustering to example_pixel_cell_clustering * Address code review comments * Fix notebook merge * Create pixel and cell cluster overlays (#431) * Initial commit * Add overlay visualizations * Add tests for pixel overlay and fix segmentation mask generation * Add cluster_col and column_prefix checks where needed * Add code to save pixel and cell masks as .tiff files in example_pixel_cell_clustering * Create datasets that integrate with remapping GUI (#447) * Add functions to generate data formats for Zak's visualization * Add option to keep the count column when aggregating the pixel cluster data * Address more code review comments * PYCODESTYLE * Separate pixel and cell clustering processes, add code to generate data files for Zak * Reassign pixel_consensus_dir back to None in example_cell_clustering.ipynb * 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 comments * Doc fix in data_utils * Adjust data_utils tests for new column names in pixel and cell cluster mask generation * Fix last code review comment (do not save two versions of weighted channel average per cell cluster) * Tested cell and pixel clustering on various cluster column pairs * Address code review comments except for no segmentation label support * Doc fix * Doc fix (round 2) * Doc fix (round 3) * Fix notebook test for pixel clustering * Support pixel clustering without segmentation images * Typo in doc * Adjust pipeline to accommodate segmentation_dir = None * Doc fix * More doc fixes * Fix notebook test * Explicitly specify max_k and cap in notebook * Documentation fixes * Fix a comment * Remove preprocessed_dir and subsetted_dir from documentation at the top * Remove TODO from pixel clustering * Update documentation in cell clustering * Update weighted cell channel average computation to take file path to weighted cell table * Adjust cell pipeline for weighted cell channel avg * Remove cell outputs from cell clustering notebook * Fix column subset * Condense cells in pixel and cell clustering process * Update notebook utils * Address one final comment * Address Candace's review comments * Address next set of Candace review comments (biggest change: z-score bug fixed) * Minor change to documentation of JSON params saved in pixel clustering * Add lower-bound capping using pmax * clusterCountsNorm to clusterCountsNormSub for consistency * Include both cell SOM and meta visualizations for weighted channel average, and nuke more mentions of hCluster_cap * Add option to specify dtype when creating the pixel matrix * Doc fixes * Add more detail for cell_table_name in cell clustering notebook * Fix comments in cell clustering * Code review comments addressed * Move z-scoring back to R, inputs to Zak's visualization now un-z-scored * Add remapping scheme to som_utils.py * Add re-mapping scheme * Fix cell clustering name * Need to add cell size normalization for weighted cell channel table * Fix tick_range None * Change default plot back to 'tab20' * Add the cmap arg back to the pixel and cell clustering notebooks * Nuke z-score in notebook * Add a test to ensure the cell table creation fails if the user provides a cell table without the required columns * Doc fixes in the cell clustering notebook * Update to take into account user renaming of meta clusters, and ensure the colors for each metacluster are consistent across every visualization * Add tests for remapping cell clusters * Fix notebook typo * Notebook update * Add test to ensure columns and SOM clusters are valid for remapping purposes * Add a test for the pixel and cell cluster overlay * Add tests to ensure the pixel meta clusters are in the right order when remapped * Add tests to ensure the cell meta clusters are in the right order * Clarify comments * Fix some docstrings related to the pixel SOM/meta cluster counts per cell * One more minor fix * More doc fixes * More notebook documentation fixes * More doc fixes * Reduce the time window for automatically rebuilding Docker on new requirements.txt to 30 minutes * Integrate interactive remapping workflow into the pixel and cell clustering pipeline (#497) * Initial commit of remapping addition to clustering pipeline * Add heatmap testing * Rework tests for file reading in metacluster_remap_gui * Add sample notebooks with re-visualization scheme * Relabel barchart, fix off-by-one meta cluster colormap error, ensure heatmap meta cluster colors are grouped together * Don't divide pixel and cell cluster counts by 1000 when displaying the bar chart * Add sample notebooks with new updated visualizations * Clarifying comment * Remap doc fixes * Remove duplicate comment about referring to documentation for cell weighting mechanism * Mega OCD * Prevent loading of .DS_Store files when generating pixel cluster masks * Bug fix in io_utils.list_files * Address all code review comments except for column names in interactive remapping * Add notebooks with seg_suffix in JSON params and cell heatmap without pixel_meta_cluster_rename_ prefix * Add test for optional prefix trimming of column names in metacluster_from_files * Patch file loading * Need to specify loading .tif and .tiff files only * Fix path * Fix path to pixel clustering * Fix notebook tests and deploy new image to Docker * Use travis_wait to force 20 minute timeout * Don't deploy on PR check anymore * Add specific pixel_output_dir and cell_output_dir folders to store intermediate files * Remove extraneous files * Remove mibi * Remove QC metric notebook test * Change function calls in notebooks_test.py * Add cell clustering test pipeline * Adjust pixel cluster test pipeline to be similar to cell cluster test pipeline * Add check_contrast = False * Remove commented notebook tests
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What is the purpose of this PR?
To verify results, we want to provide users a visualization of the average marker expression values per cluster. This is best accomplished using a heatmap.
How did you implement your changes
We have a framework for implementing heatmap visualizations, so there's not much to be done other than adding a function in
som_utilsto call it and adding the visualization inexample_flowsom_clustering.