| Age | Commit message (Expand) | Author |
|---|---|---|
| 2021-10-18 | Move `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 |
| 2021-10-18 | Move '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 |
| 2021-10-18 | Migrate `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 |
| 2021-10-14 | Fixed when model is set to account for situations with no covariates | zsloan |
| 2021-10-14 | Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R | zsloan |
| 2021-10-12 | Merge pull request #40 from zsloan/bug/fix_rqtl_covariates...Bug/fix rqtl covariates | zsloan |
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/f... | zsloan |
| 2021-10-12 | Fixes pylint errors | zsloan |
| 2021-10-12 | Fixed mypy typing errors | zsloan |
| 2021-10-12 | Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into featu... | zsloan |
| 2021-10-06 | guix.scm: Add python-flask-cors and python-plotly dependencies | BonfaceKilz |
| 2021-09-28 | Provide 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 |
| 2021-09-28 | Retrieve 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 |
| 2021-09-28 | Approximate 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 |
| 2021-09-28 | Merge pull request #38 from genenetwork/feature/wgcna_analysis...script for wgcna analysis | BonfaceKilz |
| 2021-09-27 | modify unittests | Alexander Kabui |
| 2021-09-27 | modify integration tests | Alexander Kabui |
| 2021-09-27 | add file not found exception | Alexander Kabui |
| 2021-09-27 | add tests for calling wgcna_script | Alexander Kabui |
| 2021-09-27 | return str error for exception | Alexander Kabui |
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 2021-09-27 | remove unnecessary comments and variables | Alexander Kabui |
| 2021-09-27 | Merge pull request #37 from genenetwork/heatmap_generation...Heatmap generation | BonfaceKilz |
| 2021-09-27 | Remove 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 |
| 2021-09-27 | Narrow 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 |
| 2021-09-27 | Update 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 |
| 2021-09-27 | Update 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 |
| 2021-09-25 | minor fixes for unittests | Alexander Kabui |
| 2021-09-23 | Tried to make the docstrings more consistent | zsloan |
| 2021-09-23 | Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenet... | zsloan |
| 2021-09-23 | Add typing to some functions | zsloan |
| 2021-09-23 | Add functions for getting proximal/distal markers for each pseudomarker posit... | zsloan |
| 2021-09-23 | Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't s... | zsloan |
| 2021-09-23 | Added genofile name to inputs for processing R/qtl pair-scan results, since i... | zsloan |
| 2021-09-23 | Removed quotes from beginning and end of chromosome string | zsloan |
| 2021-09-23 | Fixed a cople function calls to use the updated function names | zsloan |
| 2021-09-23 | Create pairscan_for_figure and pairscan_for_table functions that return the D... | zsloan |
| 2021-09-23 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ... | zsloan |
| 2021-09-23 | Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ... | zsloan |
| 2021-09-23 | Added pairscan boolean kwarg and process_rqtl_pairscan function for reading i... | zsloan |
| 2021-09-23 | Added line priting pair-scan results to CSV and changed the default step-size... | zsloan |
| 2021-09-23 | - Added scan_func function that determines whether scanone or scantwo...(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 | zsloan |
| 2021-09-23 | Added option for running pairscan to rqtl_wrapper.R | zsloan |
| 2021-09-23 | Fix covariates as described by Danny | zsloan |
| 2021-09-23 | add traits as columns names and pass as json input | Alexander Kabui |
| 2021-09-23 | minor fixes for endpoint | Alexander Kabui |
| 2021-09-23 | Return r error if returncode!=0 | Alexander Kabui |
| 2021-09-23 | read generated files from r and return output | Alexander Kabui |
| 2021-09-23 | check for na powerEst and use a default value | Alexander Kabui |
| 2021-09-23 | append input to output | Alexander Kabui |
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