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Pull request overview
This PR adds a YAML configuration file for a virtual database (VirtualDB) that will serve as a shared configuration for the team. The file defines repository mappings, dataset configurations, field paths, factor aliases, missing value labels, and field descriptions for various yeast genomics datasets from BrentLab and collaborators.
Changes:
- Added
brentlab_yeast_collection.yamlconfiguration file defining 7 repository configurations with multiple datasets covering binding and perturbation experiments - Configured field mappings and paths for accessing experimental data across different data sources
- Defined aliases for carbon source values and missing value labels for consistent data handling
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| BrentLab/mahendrawada_2025: | ||
| temperature_celsius: | ||
| path: experimental_conditions.temperature_celsius | ||
| dataset: | ||
| # binding | ||
| chec_mahendrawada_m2025_af_combined: | ||
| sample_id: | ||
| field: sample_id | ||
| regulator_locus_tag: | ||
| field: regulator_locus_tag | ||
| regulator_symbol: | ||
| field: regulator_symbol |
There was a problem hiding this comment.
Missing carbon_source configuration for BrentLab/mahendrawada_2025. All other binding datasets (BrentLab/callingcards, BrentLab/harbison_2004, BrentLab/rossi_2021) include carbon_source configuration, but this repository only has temperature_celsius. Consider adding carbon_source for consistency unless this experimental data genuinely lacks this information.
cmatKhan
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Mar 28, 2026
* Bump mkdocs-autorefs from 1.4.1 to 1.4.2 (#53) Bumps [mkdocs-autorefs](https://github.com/mkdocstrings/autorefs) from 1.4.1 to 1.4.2. - [Release notes](https://github.com/mkdocstrings/autorefs/releases) - [Changelog](https://github.com/mkdocstrings/autorefs/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/autorefs@1.4.1...1.4.2) --- updated-dependencies: - dependency-name: mkdocs-autorefs dependency-version: 1.4.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add neg log10 transform (#55) * adding the numeric formating back in * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * adding neg log 10 transform function. Currently producing error on dto distribution b/c of NA. This is expected behavior -- should be fixed by selecting data sets or at least exposing the reason why for user to address * adjusting global plotly formating; adding text and tabs to global dist * adding data descriptions * add docstring to create_distribution_plot --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Used .loc and created a copy of filtered dataframe to suppress SettingWithCopyWarning. (#71) * Fixed the DTO hyperlink reference. (#73) * Fixed overlapping y axis (#72) * Update plot_formatter for customize x-axis title. * updated facet column spacing to fix overlapping y-axis. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * ensure rr plots' consistency. (#75) * separated side bar into collapsible cards. (#74) * separated side bar into collapsible cards. * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/all_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Updated create_accordion_panel function. * fixed value error * Add general panel to the top. * Added accordion panels on individual regulator comparisons. * removed repetitive labels on checkbox group. * Organized the general tab in individual regulator tab. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Adding reactive connectivity btwn table and rr replicate plot (#77) * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * addressing copilot suggestions * addressing copilot * adding return typing to individual_regulator_compare_server * Added description to individual regulator tab. (#88) * Added description to individual regulator tab. * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated bulletpoints. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Split RR table into Main Selection table and Replicate Details table. Added highlight to linked selected rows in Replicate Details table. Aligned the two tables horizontally and added description in their footer. (#92) * Updated data source names. (#94) * Updated data source names. * Update tfbpshiny/utils/rank_response_replicate_plot_utils.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updated code length. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Formatted rank25 and rank50 as a percent. (#95) * Formatted rank25 and rank50 as a percent. * Update tfbpshiny/utils/safe_percentage_format.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added update_table button. (#93) * Added update_table button. * Update button style --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * adding tooltip description of columns (#98) * Restructure individual comparison tab (#105) * Restructured individual comparison tab. * Sychronized plot tabs and table tabs. * Created apply_column_names function to apply friendly column names to tables. * Update tfbpshiny/utils/apply_column_names.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added unit test for apply_column_names. * Fixed selection issue caused by changed column name. * Fixed CSS styling. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Replaced upset plot with a text box. (#112) * rearranged rr plot legend rank. (#115) * fixing merge error * fixed main table order issue. (#116) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * updated home page text. (#121) * updated home page text. * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update ir rr pages (#125) * Added descriptive text for individual comparison tab and renamed both tables including their variables. * Added subtitle showing the definition of responsiveness on the rr plot. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated the toggle and added tooltips. (#126) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Fix individual side bar (#127) * splitted replicate col selection table into general QC matrices and cc matrices. * Renamed options in the individual comparison side bar and split the checkbox groups into subsections. * Made descriptive text collapsible. (#129) * Made descriptive text collapsible. * moved the 'how to use' section out of the accordion panel. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * add hahn degron data. (#133) * This is the beginning of a new life for the tfbpshiny (#160) * updating after michael's revision requests (#130) * Bump mkdocs-autorefs from 1.4.1 to 1.4.2 (#53) Bumps [mkdocs-autorefs](https://github.com/mkdocstrings/autorefs) from 1.4.1 to 1.4.2. - [Release notes](https://github.com/mkdocstrings/autorefs/releases) - [Changelog](https://github.com/mkdocstrings/autorefs/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/autorefs@1.4.1...1.4.2) --- updated-dependencies: - dependency-name: mkdocs-autorefs dependency-version: 1.4.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add neg log10 transform (#55) * adding the numeric formating back in * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * adding neg log 10 transform function. Currently producing error on dto distribution b/c of NA. This is expected behavior -- should be fixed by selecting data sets or at least exposing the reason why for user to address * adjusting global plotly formating; adding text and tabs to global dist * adding data descriptions * add docstring to create_distribution_plot --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Used .loc and created a copy of filtered dataframe to suppress SettingWithCopyWarning. (#71) * Fixed the DTO hyperlink reference. (#73) * Fixed overlapping y axis (#72) * Update plot_formatter for customize x-axis title. * updated facet column spacing to fix overlapping y-axis. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * ensure rr plots' consistency. (#75) * separated side bar into collapsible cards. (#74) * separated side bar into collapsible cards. * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/all_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Updated create_accordion_panel function. * fixed value error * Add general panel to the top. * Added accordion panels on individual regulator comparisons. * removed repetitive labels on checkbox group. * Organized the general tab in individual regulator tab. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Adding reactive connectivity btwn table and rr replicate plot (#77) * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * addressing copilot suggestions * addressing copilot * adding return typing to individual_regulator_compare_server * Added description to individual regulator tab. (#88) * Added description to individual regulator tab. * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated bulletpoints. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Split RR table into Main Selection table and Replicate Details table. Added highlight to linked selected rows in Replicate Details table. Aligned the two tables horizontally and added description in their footer. (#92) * Updated data source names. (#94) * Updated data source names. * Update tfbpshiny/utils/rank_response_replicate_plot_utils.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updated code length. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Formatted rank25 and rank50 as a percent. (#95) * Formatted rank25 and rank50 as a percent. * Update tfbpshiny/utils/safe_percentage_format.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added update_table button. (#93) * Added update_table button. * Update button style --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * adding tooltip description of columns (#98) * Restructure individual comparison tab (#105) * Restructured individual comparison tab. * Sychronized plot tabs and table tabs. * Created apply_column_names function to apply friendly column names to tables. * Update tfbpshiny/utils/apply_column_names.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added unit test for apply_column_names. * Fixed selection issue caused by changed column name. * Fixed CSS styling. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Replaced upset plot with a text box. (#112) * rearranged rr plot legend rank. (#115) * fixing merge error * fixed main table order issue. (#116) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * updated home page text. (#121) * updated home page text. * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update ir rr pages (#125) * Added descriptive text for individual comparison tab and renamed both tables including their variables. * Added subtitle showing the definition of responsiveness on the rr plot. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated the toggle and added tooltips. (#126) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Fix individual side bar (#127) * splitted replicate col selection table into general QC matrices and cc matrices. * Renamed options in the individual comparison side bar and split the checkbox groups into subsections. * Made descriptive text collapsible. (#129) * Made descriptive text collapsible. * moved the 'how to use' section out of the accordion panel. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Mack Liao <g.liao@wustl.edu> * starting over * feat: implement UI shell with selection and analysis workspace modules (#159) Add modular Shiny UI components including: - Selection sidebar with dataset filtering - Selection matrix for dataset intersection visualization - Analysis workspace with single/comparison mode placeholders - Analysis sidebar with configuration panels - Modal dialogs for dataset details, filters, and column config - Navigation bar component - Mock data for development/testing - Updated app.py to use new modular architecture - New CSS styles replacing old style.css * starting over * feat: implement UI shell with selection and analysis workspace modules (#159) Add modular Shiny UI components including: - Selection sidebar with dataset filtering - Selection matrix for dataset intersection visualization - Analysis workspace with single/comparison mode placeholders - Analysis sidebar with configuration panels - Modal dialogs for dataset details, filters, and column config - Navigation bar component - Mock data for development/testing - Updated app.py to use new modular architecture - New CSS styles replacing old style.css * updating after michael's revision requests (#130) * Bump mkdocs-autorefs from 1.4.1 to 1.4.2 (#53) Bumps [mkdocs-autorefs](https://github.com/mkdocstrings/autorefs) from 1.4.1 to 1.4.2. - [Release notes](https://github.com/mkdocstrings/autorefs/releases) - [Changelog](https://github.com/mkdocstrings/autorefs/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/autorefs@1.4.1...1.4.2) --- updated-dependencies: - dependency-name: mkdocs-autorefs dependency-version: 1.4.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add neg log10 transform (#55) * adding the numeric formating back in * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * adding neg log 10 transform function. Currently producing error on dto distribution b/c of NA. This is expected behavior -- should be fixed by selecting data sets or at least exposing the reason why for user to address * adjusting global plotly formating; adding text and tabs to global dist * adding data descriptions * add docstring to create_distribution_plot --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Used .loc and created a copy of filtered dataframe to suppress SettingWithCopyWarning. (#71) * Fixed the DTO hyperlink reference. (#73) * Fixed overlapping y axis (#72) * Update plot_formatter for customize x-axis title. * updated facet column spacing to fix overlapping y-axis. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * ensure rr plots' consistency. (#75) * separated side bar into collapsible cards. (#74) * separated side bar into collapsible cards. * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/all_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Updated create_accordion_panel function. * fixed value error * Add general panel to the top. * Added accordion panels on individual regulator comparisons. * removed repetitive labels on checkbox group. * Organized the general tab in individual regulator tab. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Adding reactive connectivity btwn table and rr replicate plot (#77) * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * addressing copilot suggestions * addressing copilot * adding return typing to individual_regulator_compare_server * Added description to individual regulator tab. (#88) * Added description to individual regulator tab. * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated bulletpoints. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Split RR table into Main Selection table and Replicate Details table. Added highlight to linked selected rows in Replicate Details table. Aligned the two tables horizontally and added description in their footer. (#92) * Updated data source names. (#94) * Updated data source names. * Update tfbpshiny/utils/rank_response_replicate_plot_utils.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updated code length. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Formatted rank25 and rank50 as a percent. (#95) * Formatted rank25 and rank50 as a percent. * Update tfbpshiny/utils/safe_percentage_format.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added update_table button. (#93) * Added update_table button. * Update button style --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * adding tooltip description of columns (#98) * Restructure individual comparison tab (#105) * Restructured individual comparison tab. * Sychronized plot tabs and table tabs. * Created apply_column_names function to apply friendly column names to tables. * Update tfbpshiny/utils/apply_column_names.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added unit test for apply_column_names. * Fixed selection issue caused by changed column name. * Fixed CSS styling. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Replaced upset plot with a text box. (#112) * rearranged rr plot legend rank. (#115) * fixing merge error * fixed main table order issue. (#116) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * updated home page text. (#121) * updated home page text. * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update ir rr pages (#125) * Added descriptive text for individual comparison tab and renamed both tables including their variables. * Added subtitle showing the definition of responsiveness on the rr plot. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated the toggle and added tooltips. (#126) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Fix individual side bar (#127) * splitted replicate col selection table into general QC matrices and cc matrices. * Renamed options in the individual comparison side bar and split the checkbox groups into subsections. * Made descriptive text collapsible. (#129) * Made descriptive text collapsible. * moved the 'how to use' section out of the accordion panel. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Mack Liao <g.liao@wustl.edu> * starting over * updating after michael's revision requests (#130) * Bump mkdocs-autorefs from 1.4.1 to 1.4.2 (#53) Bumps [mkdocs-autorefs](https://github.com/mkdocstrings/autorefs) from 1.4.1 to 1.4.2. - [Release notes](https://github.com/mkdocstrings/autorefs/releases) - [Changelog](https://github.com/mkdocstrings/autorefs/blob/main/CHANGELOG.md) - [Commits](mkdocstrings/autorefs@1.4.1...1.4.2) --- updated-dependencies: - dependency-name: mkdocs-autorefs dependency-version: 1.4.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add neg log10 transform (#55) * adding the numeric formating back in * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tests/utils/test_safe_sci_notation.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * adding neg log 10 transform function. Currently producing error on dto distribution b/c of NA. This is expected behavior -- should be fixed by selecting data sets or at least exposing the reason why for user to address * adjusting global plotly formating; adding text and tabs to global dist * adding data descriptions * add docstring to create_distribution_plot --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Used .loc and created a copy of filtered dataframe to suppress SettingWithCopyWarning. (#71) * Fixed the DTO hyperlink reference. (#73) * Fixed overlapping y axis (#72) * Update plot_formatter for customize x-axis title. * updated facet column spacing to fix overlapping y-axis. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * ensure rr plots' consistency. (#75) * separated side bar into collapsible cards. (#74) * separated side bar into collapsible cards. * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/utils/create_accordion_panel.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/all_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Updated create_accordion_panel function. * fixed value error * Add general panel to the top. * Added accordion panels on individual regulator comparisons. * removed repetitive labels on checkbox group. * Organized the general tab in individual regulator tab. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Adding reactive connectivity btwn table and rr replicate plot (#77) * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * separating function logic to utils * random and ci are fixed in rr replicates; adding a couple dev deps for interactive work in a notebook via vscode * intermediate * intermediate * table selection works * addressing copilot suggestions * addressing copilot * adding return typing to individual_regulator_compare_server * Added description to individual regulator tab. (#88) * Added description to individual regulator tab. * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated bulletpoints. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Split RR table into Main Selection table and Replicate Details table. Added highlight to linked selected rows in Replicate Details table. Aligned the two tables horizontally and added description in their footer. (#92) * Updated data source names. (#94) * Updated data source names. * Update tfbpshiny/utils/rank_response_replicate_plot_utils.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updated code length. --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Formatted rank25 and rank50 as a percent. (#95) * Formatted rank25 and rank50 as a percent. * Update tfbpshiny/utils/safe_percentage_format.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added update_table button. (#93) * Added update_table button. * Update button style --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * adding tooltip description of columns (#98) * Restructure individual comparison tab (#105) * Restructured individual comparison tab. * Sychronized plot tabs and table tabs. * Created apply_column_names function to apply friendly column names to tables. * Update tfbpshiny/utils/apply_column_names.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update tfbpshiny/tabs/individual_regulator_compare_module.py Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Added unit test for apply_column_names. * Fixed selection issue caused by changed column name. * Fixed CSS styling. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Replaced upset plot with a text box. (#112) * rearranged rr plot legend rank. (#115) * fixing merge error * fixed main table order issue. (#116) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * updated home page text. (#121) * updated home page text. * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update tfbpshiny/tabs/home_module.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update ir rr pages (#125) * Added descriptive text for individual comparison tab and renamed both tables including their variables. * Added subtitle showing the definition of responsiveness on the rr plot. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Updated the toggle and added tooltips. (#126) Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Fix individual side bar (#127) * splitted replicate col selection table into general QC matrices and cc matrices. * Renamed options in the individual comparison side bar and split the checkbox groups into subsections. * Made descriptive text collapsible. (#129) * Made descriptive text collapsible. * moved the 'how to use' section out of the accordion panel. --------- Co-authored-by: Chase Mateusiak <chasem@wustl.edu> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Mack Liao <g.liao@wustl.edu> * starting over --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Mack Liao <g.liao@wustl.edu> * Composite page implementation (#162) * Migrated composite analysis from legacy code. Implemented dynamic boxplot. Added threshold filtering. * removing unused code --------- Co-authored-by: chasem <chasem@wustl.edu> * Added reactivity and dataflow documentations. (#161) * adding virtualDB conf (#163) * adding dbconf * adding hu * updating macos test runner on github actions * changing git source of tfbpapi * Implement DTO composite analysis with real backend data (#164) * Integrated tfbpapi on frontend; Identified potential yaml config issues. * Fix sample counts for binding datasets and add column counts - Add get_sample_count() that uses COUNT(DISTINCT sample_id) for binding datasets (Rossi, Harbison) where multiple measurements exist per sample - Add get_column_count() that returns column count from VirtualDB.describe() - Update app.py to use get_sample_count for Binding datasets and get_row_count for perturbation datasets - Update app.py to fetch and store column counts for each dataset Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Implement DTO composite analysis with real backend data - Add get_dto_config() and get_dto_data() functions to data_service.py - Filter composite analysis sidebar choices to only show datasets linked in DTO config - Use real DTO data from VirtualDB instead of mock data - Add db_name and sample_id to DTO YAML config - Set default filter threshold to 1.0 with <= operator Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Fix mypy error: add missing arguments to plot_formatter call Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> * Update tfbpshiny/modules/analysis_workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Fixed row count query issue. * Updated UI and navigation. --------- Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Feat dto comparison (#166) * Added DTO reference and plot layout switch option. * feat: transform DTO plot to -log10 scale with synced facet axes Apply -log10(pvalue) transformation to DTO empirical p-values using min non-zero value as pseudocount. Update default filter to >= 1.3 (~p < 0.05) to align with the transformed scale. Synchronize y-axis range across all facets for meaningful visual comparison. * feat: filter composite plot to shared regulators per facet In the composite distribution plot, only display regulators that exist in all color-axis sources within each facet panel. This prevents misleading comparisons where a TF appears in one source's box but is missing from another. Key details: - Source count denominator is per-facet (not global) so facets with fewer sources aren't over-filtered - Denominator includes sources with zero passing rows so strict thresholds don't silently weaken the filter - Skipped for DTO data where regulator_symbol == binding_source - Empty-state fallback when no shared regulators remain * refactor: remove Rank Response and Univariate P-value from comparison tab These methods will be re-implemented after DTO is finalized. Also renames expression_source to perturbation_source throughout. Removed: - rank_response/ directory (replicate_plot_module.py) - tabs/ directory (individual_regulator_compare_module.py) - get_mock_composite_data() and _clamp01() from mock_data.py - Rank Response and Univariate P-value radio button choices - Mock data fallback branch in _render_composite() Changed: - expression_source → perturbation_source in analysis_workspace, create_distribution_plot, and mock_data - Simplified _render_composite() to DTO-only data path - Added proper module-level logger to analysis_workspace * Added binding & perturbation correlation analysis. * refactor: remove camelCase duplicate keys from dataset dicts (#168) Standardize on snake_case only since the codebase is pure Python/Shiny with no JS frontend consuming these keys. * Adding comments (#169) * revising reactivity.md * starting to comment document and plan restructuring * removing scipy and upset deps * init * Adding comments (#170) * revising reactivity.md * starting to comment document and plan restructuring * removing scipy and upset deps * init * updating yaml * Skeletonizing the app (#172) * revised virtual_db_config * skeletonized * removing and revising * removing nav_items * refactoring modals * sidebar selection cleaned up * vdb integrated into sidebar * refining select datasets based on michael review * remove modal subdir * removing unnecessary comments from app.py * making pattern in app.py conform for servers * binding module started * clarifying readme * just instruct to pull dev * clarifying dev instructions * working with claude on binding and perturbation * working on binding and perturbation modules * bindind and perturbation basically working * ready for push to dev * Working on dockerfile terraform (#174) * debugging pip install * debugging traefik * messing with .env file * fixed author names. (#196) * Add labretriever add tests (#199) * replacing tfbpapi with labretriever. adding tests * adjustin readme * Update pyproject.toml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * update claude to specify that labretriever is downloaded from github --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updating labretriever url * adding hidden fields dict. changing field aliases and setting to labr… (#200) * adding hidden fields dict. changing field aliases and setting to labretriever head. matrix pairwise select regulators working. BUT, the regulator_locus_tag field is not populating * updating logger error to logger exception to capture traceback, and fixing an error in slugifying input ids from copilot * Bump codecov/codecov-action from 5 to 6 (#214) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5 to 6. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v5...v6) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update pytest requirement from ^8.3.5 to ^9.0.2 (#216) Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.3.5...9.0.2) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.0.2 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update shinywidgets requirement from ^0.5.2 to ^0.7.1 (#215) Updates the requirements on [shinywidgets](https://github.com/rstudio/py-shinywidgets) to permit the latest version. - [Release notes](https://github.com/rstudio/py-shinywidgets/releases) - [Changelog](https://github.com/posit-dev/py-shinywidgets/blob/main/CHANGELOG.md) - [Commits](posit-dev/py-shinywidgets@v0.5.2...v0.7.1) --- updated-dependencies: - dependency-name: shinywidgets dependency-version: 0.7.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Update ipykernel requirement from ^6.29.5 to ^7.2.0 (#210) Updates the requirements on [ipykernel](https://github.com/ipython/ipykernel) to permit the latest version. - [Release notes](https://github.com/ipython/ipykernel/releases) - [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md) - [Commits](ipython/ipykernel@v6.29.5...v7.2.0) --- updated-dependencies: - dependency-name: ipykernel dependency-version: 7.2.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * Bump mshick/add-pr-comment from 2.8.2 to 3.9.0 (#207) Bumps [mshick/add-pr-comment](https://github.com/mshick/add-pr-comment) from 2.8.2 to 3.9.0. - [Release notes](https://github.com/mshick/add-pr-comment/releases) - [Changelog](https://github.com/mshick/add-pr-comment/blob/main/CHANGELOG.md) - [Commits](mshick/add-pr-comment@b8f338c...ffd016c) --- updated-dependencies: - dependency-name: mshick/add-pr-comment dependency-version: 3.9.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Chase Mateusiak <chasem@wustl.edu> * diag modal now shows info on sample to regulator multiplicity (#206) * diag modal now shows info on sample to regulator multiplicity * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Fix scatterplot layout in binding and perturbation modules (#218) * diag modal now shows info on sample to regulator multiplicity * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions * fixing layout of scatter plots in binding and perturbation models. closes #204 * diag modal now shows info on sample to regulator multiplicity * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions * fixing layout of scatter plots in binding and perturbation models. closes #204 --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Fix/non diag modal intersect filter (#219) * diag modal now shows info on sample to regulator multiplicity * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions * fixing layout of scatter plots in binding and perturbation models. closes #204 * diag modal now shows info on sample to regulator multiplicity * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions * fixing layout of scatter plots in binding and perturbation models. closes #204 * this displays the regulator as <regulator_symbol>(<regulator_locus_tag>) and improves the non diagonal modal filter behavior * diag modal now shows info on sample to regulator multiplicity (#206) * diag modal now shows info on sample to regulator multiplicity * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Fix scatterplot layout in binding and perturbation modules (#218) * diag modal now shows info on sample to regulator multiplicity * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions * fixing layout of scatter plots in binding and perturbation models. closes #204 * diag modal now shows info on sample to regulator multiplicity * incorporating copilot suggestions * Update tfbpshiny/modules/select_datasets/server/workspace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot revisions * fixing layout of scatter plots in binding and perturbation models. closes #204 --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * diag modal now shows info on sample to regulator multiplicity * this displays the regulator as <regulator_symbol>(<regulator_locus_tag>) and improves the non diagonal modal filter behavior --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Mack Liao <g.liao@wustl.edu> Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
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just adding the vdb yaml conf. This is where we'll keep the shared config file for all of us