Add activity filtering #171
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Closed
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TODO: add top and bottom thresholds and make points gray instead of not visible |
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Update: top and bottom filtering |
azywot
reviewed
Nov 20, 2023
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Great job! 😎
Added some comments below; one additional think - I think I'd be wise to apply some button to reset the values for the thresholds (the same thing we have in (un)stacking in Hit Validation).
Totally optional: as for initial thresholds we could take min and max from the data uploaded.
Tremirre
approved these changes
Nov 22, 2023
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azywot
reviewed
Dec 1, 2023
azywot
approved these changes
Dec 3, 2023
Tremirre
approved these changes
Dec 3, 2023
zuzg
added a commit
that referenced
this pull request
Dec 14, 2023
* feat: store user compounds data in the filesystem * test: add unit tests to LocalFileStorage * chore: add missing newlines, remove extra newlines * Add base plate class * Add plate reading from dir * add missing dependencies * echo file processing * add echo files parser + tests * update dependencies v2 * add missing newlines * add missing newlines :)) * Add docs * add suggestions * resolve styling issue * Refactor BMG files reading * Add tests * Add summary visualizations * Modify summary tuple method * Fix docstring * Modify test for plate * Optimize dataframe reading * Define PlateSummary type * 72 set up pre-commit (#75) * Add pre-commit * Add black workflow * Reformat files * 73 detect outliers control values (#77) * Fix colours in control values plot * Add outliers detection * Add test for outliers * Apply review fixes * Fix tests * Separate plate_array from df * Fix typing and docs * Change plot types * Change plates viz to plotly * 74 inhibitionactivation values (#79) * Fix colours in control values plot * Add outliers detection * Add test for outliers * Apply review fixes * Fix tests * Separate plate_array from df * compute inhibition/activation * merge activation/inhibition with echo files * check upon the values * fix combining echo bmg files * drop unnecessary columns * remove outliers from the resultant df * split compounds/controls, add z-score * add visualizations * add tests * improve docs and plot --------- Co-authored-by: Zuza Gawrysiak <[email protected]> * closes #80 general restructuring (#81) * chore: merge src into dashboard * update: set basic pages structure * update: add stages placeholders to Primary Screening process * chore: for the time being move old code to LEGACY folder, remove outdated layouts * feat: add decorator for error handling * fix: correct import in a unit test * update: make data_folder a class attribute to facilitate global configuration * fix: correct LocalFileStorage test * chore: remove redundant style attr * Plot improvements (#85) * Filter low quality plates * Make plot grid size modifiable * Add z per plate plot * Change template to plotly_white * Apply review fixes * Add plotly template as const * Stage 1 and Stage 4 uploading (#86) * Add reading ioFile in bmg * Saving BML in Storage * Add echo reading * Add coments * Resolve tests problems * Pre-commit * Pre-commit changes * Solve problems * Bmg refactor * Bmg refactor * Echo parser refactor * Fix * Fix comment * 82 implement stage 2 (#90) * fix: add correct name to elements property, set stages container style to take full width * fix: subplots' titles not visibile correctly in heatmaps plot * feat: implement paginated heatmap plates viewer * add datatable for statistics preview, extend controls * add docstring * fix: sizing on smaller screens * Add stage 3 in dash (#89) * Add stage 3 in dash * Add z threshold slider * Refactor filtering lq plates * Change return annotation * 83 implement stage 5 in dashboard (#92) * add stage 5 table * add plots ad datatable * add interactive z-score * change act/inh/zscore plots * add RangeSlider * change data table styling * resolve imports/typos * Add stage 3 improvements (#95) * Change view of stage 1 and 4 (#93) * Change view of stage 1 and 4 * Resolve problems * Divide info into two parts * Change view * Change view * closes 96 update stage 2 layout (#97) * adjust stage 2 layout * hide plot controls * disable zooming and panning on heatmap plots * closes 98 add report stage revamp process controls (#99) * add placeholder for stage 6 * add functional controls component * remove old function for creating controls component * add icons to prev/next stage buttons * add border to controls component * remove commented code * closes 101 add correlation process (#104) * chore: rename primary_screening package to screening * update: rename primary-screening process page to screening * update: dummy element to be created per-process page * feat: add correlation process basis * feat: fill in first stage html * feat: add files parsing and validation placeholder * feat: implement remaining stages * Export screening results to csv file (#107) * add save report v1 * download echo_bmg_combined.csv * add custom csv name * clean callbacks.py * update delete_file * remove custom file name * remove imports * fix csv export (#112) * Report generation (#108) * Generate simple raport * Add storage for report data * Add plot in raport * Resolve problems * Clean code * Add secondary screening plots (#103) * Add secondary screening plots * Add concentration calculation * Fix docstring * Save report to download (#113) * 115 deanonymize compounds (#117) * Add eos * Update regex * Add eos to correlation stage * Fix test * Fix well naming issues * Remove unnecessary changes * Fix test * Remove rows without eos * closes 116 UI for hit validation process (#119) * Add hit validation process page stages, implement first stage * add parameters setting to first stage * adjust parameter change callback * implement second stage of hit validation process * remove step from concentration bounds inputs * reorder pages in nav bar * Update INH/ACT/Z-SCORE plots (#114) * add area charts * add hline * add ranges to act/inh * add filter criteria * add well/plate distinction * filter compounds to save * alter serialization * include bmg controls * fix test * fix test #2 * Pipeline check and fixes (#120) * change z-score calculation * handle different echo files * alter act/inh * fix test * fix tests & add exceptions button * filter low quality plates * change the origin * Add url to EOS datable (#129) * Add eos url * Fix styling * Save app settings to JSON file (#131) * Save json from primmary screening * clean * pre-commit * Rename methods and dicts * Add saving settings in correlation and hit validation * Style buttons * closes 126 implement third process (#133) * remove .venv from git tracking * implement basic parsing * implement file parsing and graph creation * implement csv downloading * remove unneeded files --------- Co-authored-by: njytwf <[email protected]> * closes 138 control hit plot (#139) * fix initial process callbacks not setting stored uuid * implement stacking control * round top/bottom values * closes 140 configuration for hit determination (#142) * ui for controls * parametrize hit determination * connect state variables with the configuration callback * remove whitespace * Add plots to screening report (#143) * Add data projections (#132) * update combining process * add data projection process * add dropdowns * add eos links, save file * remove an outdated test * alter combine_assays_for_projection * add loading sign/dynamic table * add controls to the report * Revert "add controls to the report" This reverts commit 14328d2. * remove apply button * add controls to the plot * revert legacy change * include both ACT & INH to projections * update umap package version * remove legacy, return uuid initially * Implement SMILES predictor (#141) * Train xgboost * Predict on ecbd data * Add smoter * Save preds to pq * Fix plotted eoses (#151) * Add predictions to dashboard (#146) * Add predictions to dashboard * Add SMILES plotting * Change predictions file to pq * Add missing requirements * Comment out umap (#153) * Comment out umap * Format notebook * Update default projection * merge inh/act into feature (#144) * merge inh/act into feature * remove functools.partial wrapper * 136 Save individual EOS report (#155) * Add statistics * Create report * Add concentration for 50% modulation * Uppercase letter * closes 147 app redesign 💅💅 (#154) * navbar and homepage re-design * make logo smaller, set correct logo src * redesign about page * reformat file * add smartart to about page * Correlation report (#157) * Create report correlation * Create report correlation * Fix Correlation stage * Add typing * Fix concentration_50 statistic (#161) * Create report correlation * Fix concentration_50 * closes 159 minor UI adjustments (#160) * add link * make main pages responsive * hit browser styling fixes * adjust stacking controls styling * replace buttons list with searchable dropdown for hit browser component selection * fix individual report generation * Add structural similarity (#156) * Add structural similarity * Small refactor * Fix file upload * Improve clustering * Move plot to plots * Update colors * Export eos plots to the final report (#168) * add report generation * add dependencies * alter saved plots * fix: handle case when last page is of size 0 (#169) * closes 165 update projections (#170) * add 3d projection plots * facilitate selected datapoints download for Visualization stage * facilitate selected datapoints download for Similarity stage * disable "Download selected" buttons when 3d plotting enabled * 147 app redesign v2 (#162) * unify plots view, add loaders * add page blockers * divide eos/echo loaders * remove unnecessary comments * change select file color * correct heatmap loader * alter upload text * add info icon * alter info icon position * fix info icon * Add ML experiment setup (#176) * Add ml experiment setup * Add feature selection, hp tuning and docs * Split projection stage (#174) * split stages * add projections processes descriptions * closes 166 minor styling (#175) * unify precision in screening process * fix unit display for concentration50 * add kaleido dependency * unify precision in data projection process * add thousands delimiter * restyle controls to include process name * replace screening statistics charts with bar plots * adjust styling for tooltip * allow to extend tooltip with custom styling * add bottom padding to page container * add tooltips to hit validation process * move tooltip annotation to components module * add tooltips to Screening process * reduce process title size * add tooltips to data projection process * extend docstring of the annotating function * add tooltips to correlation process * adjust concentration slider desc * update sliders tooltip descriptions for correlation * adjust coloring of mean value bar plots * add missing information in various descriptions * render error message when user uploads less than 3 screening files in data projection process * readd missing stage * restore controls chart to scatter plot * Update version (#179) * Update version * Remove dev * fix responsiveness (#181) * Add reproducibility (#177) * Reproducing Screening and Correlation * Reproducing Hit Validation * Remove checkbox changning * Change gitignore * Add alerts * Resolve * Reports refactor (#178) * Reproducing Screening and Correlation * Reproducing Hit Validation * Remove checkbox changning * Create Header in reports * Merge develop * restore changes from broken branch (#185) * After testing adjustments (#184) * add projections smiles info * add modulation_50/concentration_50 to report * add low quality plate csv * fix test * correct typos/pca_smiles_summary * remove pca_smiles_summary * Add activity filtering (#171) * Add activity filtering * Update layout * Add top and bottom thresholds * Add lines and separate threshold change * Add save button * Move button and rename cols * Update button * Refactor uploading files (#187) * Add text on upload * Individual text * Refactor * Add missing words * Resolve merge problem * Bump version (#188) --------- Co-authored-by: Bartosz Stachowiak <[email protected]> Co-authored-by: Bartosz Stachowiak <[email protected]> Co-authored-by: azywot <[email protected]> Co-authored-by: AndrzejKaj <[email protected]> Co-authored-by: Agata <[email protected]> Co-authored-by: njytwf <[email protected]>
zuzg
added a commit
that referenced
this pull request
Dec 19, 2023
* Release v2.1.0 (#189) * feat: store user compounds data in the filesystem * test: add unit tests to LocalFileStorage * chore: add missing newlines, remove extra newlines * Add base plate class * Add plate reading from dir * add missing dependencies * echo file processing * add echo files parser + tests * update dependencies v2 * add missing newlines * add missing newlines :)) * Add docs * add suggestions * resolve styling issue * Refactor BMG files reading * Add tests * Add summary visualizations * Modify summary tuple method * Fix docstring * Modify test for plate * Optimize dataframe reading * Define PlateSummary type * 72 set up pre-commit (#75) * Add pre-commit * Add black workflow * Reformat files * 73 detect outliers control values (#77) * Fix colours in control values plot * Add outliers detection * Add test for outliers * Apply review fixes * Fix tests * Separate plate_array from df * Fix typing and docs * Change plot types * Change plates viz to plotly * 74 inhibitionactivation values (#79) * Fix colours in control values plot * Add outliers detection * Add test for outliers * Apply review fixes * Fix tests * Separate plate_array from df * compute inhibition/activation * merge activation/inhibition with echo files * check upon the values * fix combining echo bmg files * drop unnecessary columns * remove outliers from the resultant df * split compounds/controls, add z-score * add visualizations * add tests * improve docs and plot --------- Co-authored-by: Zuza Gawrysiak <[email protected]> * closes #80 general restructuring (#81) * chore: merge src into dashboard * update: set basic pages structure * update: add stages placeholders to Primary Screening process * chore: for the time being move old code to LEGACY folder, remove outdated layouts * feat: add decorator for error handling * fix: correct import in a unit test * update: make data_folder a class attribute to facilitate global configuration * fix: correct LocalFileStorage test * chore: remove redundant style attr * Plot improvements (#85) * Filter low quality plates * Make plot grid size modifiable * Add z per plate plot * Change template to plotly_white * Apply review fixes * Add plotly template as const * Stage 1 and Stage 4 uploading (#86) * Add reading ioFile in bmg * Saving BML in Storage * Add echo reading * Add coments * Resolve tests problems * Pre-commit * Pre-commit changes * Solve problems * Bmg refactor * Bmg refactor * Echo parser refactor * Fix * Fix comment * 82 implement stage 2 (#90) * fix: add correct name to elements property, set stages container style to take full width * fix: subplots' titles not visibile correctly in heatmaps plot * feat: implement paginated heatmap plates viewer * add datatable for statistics preview, extend controls * add docstring * fix: sizing on smaller screens * Add stage 3 in dash (#89) * Add stage 3 in dash * Add z threshold slider * Refactor filtering lq plates * Change return annotation * 83 implement stage 5 in dashboard (#92) * add stage 5 table * add plots ad datatable * add interactive z-score * change act/inh/zscore plots * add RangeSlider * change data table styling * resolve imports/typos * Add stage 3 improvements (#95) * Change view of stage 1 and 4 (#93) * Change view of stage 1 and 4 * Resolve problems * Divide info into two parts * Change view * Change view * closes 96 update stage 2 layout (#97) * adjust stage 2 layout * hide plot controls * disable zooming and panning on heatmap plots * closes 98 add report stage revamp process controls (#99) * add placeholder for stage 6 * add functional controls component * remove old function for creating controls component * add icons to prev/next stage buttons * add border to controls component * remove commented code * closes 101 add correlation process (#104) * chore: rename primary_screening package to screening * update: rename primary-screening process page to screening * update: dummy element to be created per-process page * feat: add correlation process basis * feat: fill in first stage html * feat: add files parsing and validation placeholder * feat: implement remaining stages * Export screening results to csv file (#107) * add save report v1 * download echo_bmg_combined.csv * add custom csv name * clean callbacks.py * update delete_file * remove custom file name * remove imports * fix csv export (#112) * Report generation (#108) * Generate simple raport * Add storage for report data * Add plot in raport * Resolve problems * Clean code * Add secondary screening plots (#103) * Add secondary screening plots * Add concentration calculation * Fix docstring * Save report to download (#113) * 115 deanonymize compounds (#117) * Add eos * Update regex * Add eos to correlation stage * Fix test * Fix well naming issues * Remove unnecessary changes * Fix test * Remove rows without eos * closes 116 UI for hit validation process (#119) * Add hit validation process page stages, implement first stage * add parameters setting to first stage * adjust parameter change callback * implement second stage of hit validation process * remove step from concentration bounds inputs * reorder pages in nav bar * Update INH/ACT/Z-SCORE plots (#114) * add area charts * add hline * add ranges to act/inh * add filter criteria * add well/plate distinction * filter compounds to save * alter serialization * include bmg controls * fix test * fix test #2 * Pipeline check and fixes (#120) * change z-score calculation * handle different echo files * alter act/inh * fix test * fix tests & add exceptions button * filter low quality plates * change the origin * Add url to EOS datable (#129) * Add eos url * Fix styling * Save app settings to JSON file (#131) * Save json from primmary screening * clean * pre-commit * Rename methods and dicts * Add saving settings in correlation and hit validation * Style buttons * closes 126 implement third process (#133) * remove .venv from git tracking * implement basic parsing * implement file parsing and graph creation * implement csv downloading * remove unneeded files --------- Co-authored-by: njytwf <[email protected]> * closes 138 control hit plot (#139) * fix initial process callbacks not setting stored uuid * implement stacking control * round top/bottom values * closes 140 configuration for hit determination (#142) * ui for controls * parametrize hit determination * connect state variables with the configuration callback * remove whitespace * Add plots to screening report (#143) * Add data projections (#132) * update combining process * add data projection process * add dropdowns * add eos links, save file * remove an outdated test * alter combine_assays_for_projection * add loading sign/dynamic table * add controls to the report * Revert "add controls to the report" This reverts commit 14328d2. * remove apply button * add controls to the plot * revert legacy change * include both ACT & INH to projections * update umap package version * remove legacy, return uuid initially * Implement SMILES predictor (#141) * Train xgboost * Predict on ecbd data * Add smoter * Save preds to pq * Fix plotted eoses (#151) * Add predictions to dashboard (#146) * Add predictions to dashboard * Add SMILES plotting * Change predictions file to pq * Add missing requirements * Comment out umap (#153) * Comment out umap * Format notebook * Update default projection * merge inh/act into feature (#144) * merge inh/act into feature * remove functools.partial wrapper * 136 Save individual EOS report (#155) * Add statistics * Create report * Add concentration for 50% modulation * Uppercase letter * closes 147 app redesign 💅💅 (#154) * navbar and homepage re-design * make logo smaller, set correct logo src * redesign about page * reformat file * add smartart to about page * Correlation report (#157) * Create report correlation * Create report correlation * Fix Correlation stage * Add typing * Fix concentration_50 statistic (#161) * Create report correlation * Fix concentration_50 * closes 159 minor UI adjustments (#160) * add link * make main pages responsive * hit browser styling fixes * adjust stacking controls styling * replace buttons list with searchable dropdown for hit browser component selection * fix individual report generation * Add structural similarity (#156) * Add structural similarity * Small refactor * Fix file upload * Improve clustering * Move plot to plots * Update colors * Export eos plots to the final report (#168) * add report generation * add dependencies * alter saved plots * fix: handle case when last page is of size 0 (#169) * closes 165 update projections (#170) * add 3d projection plots * facilitate selected datapoints download for Visualization stage * facilitate selected datapoints download for Similarity stage * disable "Download selected" buttons when 3d plotting enabled * 147 app redesign v2 (#162) * unify plots view, add loaders * add page blockers * divide eos/echo loaders * remove unnecessary comments * change select file color * correct heatmap loader * alter upload text * add info icon * alter info icon position * fix info icon * Add ML experiment setup (#176) * Add ml experiment setup * Add feature selection, hp tuning and docs * Split projection stage (#174) * split stages * add projections processes descriptions * closes 166 minor styling (#175) * unify precision in screening process * fix unit display for concentration50 * add kaleido dependency * unify precision in data projection process * add thousands delimiter * restyle controls to include process name * replace screening statistics charts with bar plots * adjust styling for tooltip * allow to extend tooltip with custom styling * add bottom padding to page container * add tooltips to hit validation process * move tooltip annotation to components module * add tooltips to Screening process * reduce process title size * add tooltips to data projection process * extend docstring of the annotating function * add tooltips to correlation process * adjust concentration slider desc * update sliders tooltip descriptions for correlation * adjust coloring of mean value bar plots * add missing information in various descriptions * render error message when user uploads less than 3 screening files in data projection process * readd missing stage * restore controls chart to scatter plot * Update version (#179) * Update version * Remove dev * fix responsiveness (#181) * Add reproducibility (#177) * Reproducing Screening and Correlation * Reproducing Hit Validation * Remove checkbox changning * Change gitignore * Add alerts * Resolve * Reports refactor (#178) * Reproducing Screening and Correlation * Reproducing Hit Validation * Remove checkbox changning * Create Header in reports * Merge develop * restore changes from broken branch (#185) * After testing adjustments (#184) * add projections smiles info * add modulation_50/concentration_50 to report * add low quality plate csv * fix test * correct typos/pca_smiles_summary * remove pca_smiles_summary * Add activity filtering (#171) * Add activity filtering * Update layout * Add top and bottom thresholds * Add lines and separate threshold change * Add save button * Move button and rename cols * Update button * Refactor uploading files (#187) * Add text on upload * Individual text * Refactor * Add missing words * Resolve merge problem * Bump version (#188) --------- Co-authored-by: Bartosz Stachowiak <[email protected]> Co-authored-by: Bartosz Stachowiak <[email protected]> Co-authored-by: azywot <[email protected]> Co-authored-by: AndrzejKaj <[email protected]> Co-authored-by: Agata <[email protected]> Co-authored-by: njytwf <[email protected]> * Add option to save processed dataset * Update model params --------- Co-authored-by: Bartosz Stachowiak <[email protected]> Co-authored-by: Bartosz Stachowiak <[email protected]> Co-authored-by: azywot <[email protected]> Co-authored-by: AndrzejKaj <[email protected]> Co-authored-by: Agata <[email protected]> Co-authored-by: njytwf <[email protected]>
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Fixes: #167
