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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
2021-10-12Fixes pylint errorszsloan
2021-10-12Fixed mypy typing errorszsloan
2021-10-12Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_pairscan
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
2021-09-23Tried to make the docstrings more consistentzsloan
2021-09-23Merge branch 'feature/add_rqtl_pairscan' of ↵zsloan
https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan
2021-09-23Add typing to some functionszsloan
2021-09-23Add functions for getting proximal/distal markers for each pseudomarker ↵zsloan
position in pair-scan results + return only the sorted top 500 results
2021-09-23Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't ↵zsloan
selected
2021-09-23Added genofile name to inputs for processing R/qtl pair-scan results, since ↵zsloan
it's needed to store the proximal/distal markers for each position
2021-09-23Removed quotes from beginning and end of chromosome stringzsloan
2021-09-23Fixed a cople function calls to use the updated function nameszsloan
2021-09-23Create pairscan_for_figure and pairscan_for_table functions that return the ↵zsloan
Dict and List respectively used for the pair scan figure and the table showing the results
2021-09-23Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ↵zsloan
we need the list of markers/pseudomarkers and their positions)
2021-09-23Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ↵zsloan
api/rqtl.py
2021-09-23Added pairscan boolean kwarg and process_rqtl_pairscan function for reading ↵zsloan
in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan
2021-09-23Added line priting pair-scan results to CSV and changed the default ↵zsloan
step-size to 10cM for pair-scan
2021-09-23- Added scan_func function that determines whether scanone or scantwozsloan
(pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints
2021-09-23Added option for running pairscan to rqtl_wrapper.Rzsloan
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
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