| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2021-09-28 | Retrieve loci names ordered by chromosomes | Frederick 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. | |||
| 2021-09-28 | Approximate single-spectrum colour scale in GN1 | Frederick 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. | |||
| 2021-09-28 | Merge pull request #38 from genenetwork/feature/wgcna_analysis | BonfaceKilz | |
| script for wgcna analysis | |||
| 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 | BonfaceKilz | |
| Heatmap generation | |||
| 2021-09-27 | Remove 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 | |||
| 2021-09-27 | Narrow the exception and add comments | Frederick 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 | |||
| 2021-09-27 | Update 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 | |||
| 2021-09-27 | Update 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 | |||
| 2021-09-25 | 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 ↵ | zsloan | |
| https://github.com/zsloan/genenetwork3 into feature/add_rqtl_pairscan | |||
| 2021-09-23 | Add typing to some functions | zsloan | |
| 2021-09-23 | Add functions for getting proximal/distal markers for each pseudomarker ↵ | zsloan | |
| position in pair-scan results + return only the sorted top 500 results | |||
| 2021-09-23 | Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't ↵ | zsloan | |
| selected | |||
| 2021-09-23 | Added 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 | |||
| 2021-09-23 | 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 ↵ | zsloan | |
| Dict and List respectively used for the pair scan figure and the table showing the results | |||
| 2021-09-23 | Updated 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) | |||
| 2021-09-23 | Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ↵ | zsloan | |
| api/rqtl.py | |||
| 2021-09-23 | Added 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 | |||
| 2021-09-23 | Added 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 scantwo | zsloan | |
| (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 | |||
| 2021-09-23 | 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 | |
| 2021-09-23 | sample output data | Alexander Kabui | |
| 2021-09-23 | validate required output | Alexander Kabui | |
| 2021-09-23 | add mock test data for script | Alexander Kabui | |
| 2021-09-23 | pass json file path as an arg | Alexander Kabui | |
| 2021-09-23 | pass other variables from user input for network constr | Alexander Kabui | |
| 2021-09-23 | add rjson dependency | Alexander Kabui | |
| 2021-09-23 | load data from json file and and convert to dt | Alexander Kabui | |
| 2021-09-23 | Add missing dependencies causing pylint to fail | Frederick Muriuki Muriithi | |
| * Add some dependencies used by the system that were missing in the test environment, leading to the pylint step failing. | |||
| 2021-09-23 | Refactor: Move common sample data to separate file | Frederick 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. | |||
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi | |
| 2021-09-22 | Fix typing issues | Frederick Muriuki Muriithi | |
| * Ignore some errors * Update typing definitions for some portions of code * Add missing imports | |||
| 2021-09-22 | Fix pylint errors | Frederick 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. | |||
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