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2021-10-19Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-corre...Frederick Muriuki Muriithi
2021-10-19Implement remaining `fix_samples` functionality...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `fix_samples` function * tests/unit/test_partial_correlations.py: implement tests for `fix_samples` function Implement the remaining partial migration for the `web.webqtl.correlation.correlationFunction.fixStrain` function in GN1. Frederick Muriuki Muriithi
2021-10-19Fix some linting issuesFrederick Muriuki Muriithi
2021-10-19Allow CORS_ORIGINS to be configurable via the environment...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * gn3/app.py: setup CORS after all the configuration sources are loaded. * gn3/settings.py: Parse CORS_ORIGINS from the environment variables. Enable the CORS_ORIGINS configuration to be set in the environment variables to give the application some flexibility when launching. Frederick Muriuki Muriithi
2021-10-19Enable vertical and horizontal heatmaps...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Update the request endpoint, so that it produces a vertical or horizontal heatmap depending on the user's request. Frederick Muriuki Muriithi
2021-10-19Enable vertical orientation of heatmaps...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Update the code to enable the generation of the heatmap in both the horizontal and vertical orientations. Frederick Muriuki Muriithi
2021-10-19Swap axis labels...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Switch the axis labels to make them less confusing for the user. Frederick Muriuki Muriithi
2021-10-19Add typing. Simplify arguments....Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Add type-hints to the functions * Merge the axis data and labels to simpler dict arguments to reduce number of parameters to the function. Frederick Muriuki Muriithi
2021-10-19Remove file I/O statements...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi * Remove file I/O from the function. If file I/O is needed, it will be provided outside of this function. Frederick Muriuki Muriithi
2021-10-19Implement `dictify_by_samples`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: implement `dictify_by_samples` function * tests/unit/test_partial_correlations.py: implement tests for `dictify_by_samples` function Implement the `dictify_by_samples` function as a partial migration of the `web.webqtl.correlation.correlationFunction.fixStrains` function from GN1. Frederick Muriuki Muriithi
2021-10-18Disable pylint issue...* Disable minor pylint issue. Frederick Muriuki Muriithi
2021-10-18Implement `control_samples` function as is in GN1...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement `control_samples` function * tests/unit/test_partial_correlations.py: add tests for `control_samples` function Implement the function `control_samples` and make it mostly bug-compatible with the `web/webqtl/correlation/correlationFunction.controlStrain` function in GN1. This implementation in GN3 does not do any calls to the database. It will rely on other functions to provide the data from the database to it. Frederick Muriuki Muriithi
2021-10-18Move `export_informative` function to `gn3.db.traits` module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move `export_informative` function here * gn3/partial_correlations.py: Remove `export_informative` function * tests/unit/db/test_traits.py: Move `export_informative` function tests here * tests/unit/test_partial_correlations.py: Remove `export_informative` function tests The `export_informative` function relates more to the traits than to the partial correlations, and could find use in more than just the partial correlations stuff. This commit moves the function to the more traits-specific `gn3.db.traits` module. Frederick Muriuki Muriithi
2021-10-18Move 'export_trait_data' to 'gn3.db.traits' module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move function `export_trait_data` here * gn3/heatmaps.py: Remove function `export_trait_data` * tests/unit/db/test_traits.py: Move function `export_trait_data` tests here * tests/unit/test_heatmaps.py: Remove function `export_trait_data` here Function `export_trait_data` more closely corresponds to the traits and is used in more than just the `gn3.heatmaps` module. This commit moves the relevant code over to the `gn3.db.traits` module and also moves the tests to the corresponding tests modules. Frederick Muriuki Muriithi
2021-10-18Migrate `export_informative` function...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/partial_correlations.py: Implement a mostly, bug-compatible `export_informative` function as part of migrating the partial correlations feature over to GN3 from GN1 * tests/unit/test_partial_correlations.py: Implement tests to ensure the code work in a similar manner as that one in GN1. Frederick Muriuki Muriithi
2021-10-14Fixed when model is set to account for situations with no covariateszsloan
2021-10-14Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.Rzsloan
2021-10-12Merge pull request #40 from zsloan/bug/fix_rqtl_covariates...Bug/fix rqtl covariateszsloan
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f...zsloan
2021-10-06guix.scm: Add python-flask-cors and python-plotly dependenciesBonfaceKilz
2021-09-28Provide loci names to heatmap...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide the loci names to the heatmaps so that hovering over the heatmap cells displays the associated locus name. Frederick Muriuki Muriithi
2021-09-28Retrieve loci names ordered by chromosomes...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps.py: implement function * tests/unit/test_heatmaps.py: add test Add a function to retrieve the loci names from the traits, ordered by chromosomes, in alphabetical order. This is useful to provide the user with more information on hovering over the heatmap cells: each cell will now display the locus name, trait name and value associated with it. Frederick Muriuki Muriithi
2021-09-28Approximate single-spectrum colour scale in GN1...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * To provide a somewhat similar experience to GeneNetwork1, this commit approximates the single-spectrum colour scale in GeneNetwork1 for the heatmaps in GeneNetwork3. Work to get the multiple-spectrum colour sc(ales/hemes) will be done in other commits, since that might require digging even deeper into Plotly's guts to figure out. Frederick Muriuki Muriithi
2021-09-28Merge pull request #38 from genenetwork/feature/wgcna_analysis...script for wgcna analysisBonfaceKilz
2021-09-27modify unittestsAlexander Kabui
2021-09-27modify integration testsAlexander Kabui
2021-09-27add file not found exceptionAlexander Kabui
2021-09-27add tests for calling wgcna_scriptAlexander Kabui
2021-09-27return str error for exceptionAlexander Kabui
2021-09-27fix merge conflictsAlexander Kabui
2021-09-27remove unnecessary comments and variablesAlexander Kabui
2021-09-27Merge pull request #37 from genenetwork/heatmap_generation...Heatmap generationBonfaceKilz
2021-09-27Remove unnecessary variable....Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix issue according to review https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714549781 Frederick Muriuki Muriithi
2021-09-27Narrow the exception and add comments...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Only catch the `FileExistsError` allowing any other exception to pass through. This tries to conform a little to the review at https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714552696 Frederick Muriuki Muriithi
2021-09-27Update terminology: `riset` to `group`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update terminology to use the appropriate domain terminology according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744 Frederick Muriuki Muriithi
2021-09-27Update terminology: `strain` to `sample`...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the terminology used: use `sample` in place of `strain` according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306 Frederick Muriuki Muriithi
2021-09-25minor fixes for unittestsAlexander Kabui
2021-09-23Fix covariates as described by Dannyzsloan
2021-09-23add traits as columns names and pass as json inputAlexander Kabui
2021-09-23minor fixes for endpointAlexander Kabui
2021-09-23Return r error if returncode!=0Alexander Kabui
2021-09-23read generated files from r and return outputAlexander Kabui
2021-09-23check for na powerEst and use a default valueAlexander Kabui
2021-09-23append input to outputAlexander Kabui
2021-09-23sample output dataAlexander Kabui
2021-09-23validate required outputAlexander Kabui
2021-09-23add mock test data for scriptAlexander Kabui
2021-09-23pass json file path as an argAlexander Kabui
2021-09-23pass other variables from user input for network constrAlexander Kabui
2021-09-23add rjson dependencyAlexander Kabui