| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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. | |||
| 2021-09-22 | Update check: Heatmaps need at least 2 items | Frederick 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. | |||
| 2021-09-22 | Return serialized plotly figure | Frederick 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. | |||
| 2021-09-22 | add init tests for call to script | Alexander Kabui | |
| 2021-09-22 | add required wgcna dependencies to guix.scm | Alexander Kabui | |
| 2021-09-22 | jsonify results | Alexander Kabui | |
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