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2021-10-19Implement remaining `fix_samples` functionalityFrederick Muriuki Muriithi
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.
2021-10-19Implement `dictify_by_samples`Frederick Muriuki Muriithi
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.
2021-10-18Disable pylint issueFrederick Muriuki Muriithi
* Disable minor pylint issue.
2021-10-18Implement `control_samples` function as is in GN1Frederick Muriuki Muriithi
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.
2021-10-18Move `export_informative` function to `gn3.db.traits` moduleFrederick Muriuki Muriithi
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.
2021-10-18Move 'export_trait_data' to 'gn3.db.traits' moduleFrederick Muriuki Muriithi
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.
2021-10-18Migrate `export_informative` functionFrederick Muriuki Muriithi
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.
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_covariateszsloan
Bug/fix rqtl covariates
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
bug/fix_rqtl_covariates
2021-10-06guix.scm: Add python-flask-cors and python-plotly dependenciesBonfaceKilz
2021-09-28Provide loci names to heatmapFrederick Muriuki Muriithi
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.
2021-09-28Retrieve loci names ordered by chromosomesFrederick Muriuki Muriithi
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.
2021-09-28Approximate single-spectrum colour scale in GN1Frederick Muriuki Muriithi
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.
2021-09-28Merge pull request #38 from genenetwork/feature/wgcna_analysisBonfaceKilz
script for wgcna analysis
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_generationBonfaceKilz
Heatmap generation
2021-09-27Remove unnecessary variable.Frederick Muriuki Muriithi
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
2021-09-27Narrow the exception and add commentsFrederick Muriuki Muriithi
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
2021-09-27Update terminology: `riset` to `group`Frederick Muriuki Muriithi
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
2021-09-27Update terminology: `strain` to `sample`Frederick Muriuki Muriithi
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
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
2021-09-23load data from json file and and convert to dtAlexander Kabui
2021-09-23Add missing dependencies causing pylint to failFrederick Muriuki Muriithi
* Add some dependencies used by the system that were missing in the test environment, leading to the pylint step failing.
2021-09-23Refactor: Move common sample data to separate fileFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move common sample test data into a separate file where it can be imported from, to prevent pylint error R0801 which proved tricky to silence in any other way.
2021-09-22Fix more pylint errorsFrederick Muriuki Muriithi
2021-09-22Fix typing issuesFrederick Muriuki Muriithi
* Ignore some errors * Update typing definitions for some portions of code * Add missing imports
2021-09-22Fix pylint errorsFrederick Muriuki Muriithi
* Add missing function and module docstrings * Remove unused imports * Fix import order * Rework some code sections to fix issues * Disable some pylint errors.
2021-09-22Update check: Heatmaps need at least 2 itemsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the check to look for at least 2 traits before trying to generate the heatmap.
2021-09-22Return serialized plotly figureFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/api/heatmaps.py: Serialize the figure to JSON * gn3/heatmaps.py: Return the figure object Serialize the Plotly figure into JSON, and return that, so that it can be used on the client to display the image.
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