| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 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...* Add some dependencies used by the system that were missing in the test
environment, leading to the pylint step failing.
| Frederick Muriuki Muriithi |
| 2021-09-23 | Refactor: Move common sample data to separate file...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.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix more pylint errors | Frederick Muriuki Muriithi |
| 2021-09-22 | Fix typing issues...* Ignore some errors
* Update typing definitions for some portions of code
* Add missing imports
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix pylint errors...* Add missing function and module docstrings
* Remove unused imports
* Fix import order
* Rework some code sections to fix issues
* Disable some pylint errors.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Update check: Heatmaps need at least 2 items...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.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Return serialized plotly figure...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.
| Frederick Muriuki Muriithi |
| 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 |
| 2021-09-22 | init endpoint tests for wgcna | Alexander Kabui |
| 2021-09-20 | Enable Cross-Origin Resource Sharing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Fix bugs in data parsing
* gn3/app.py: enable CORS
* gn3/settings.py: add flask-cors configurations
* guix.scm: Add flask-cors dependency
For easier testing of the heatmaps generation feature, this commit activates
the cross-origin resource sharing for all "localhost" origins.
| Frederick Muriuki Muriithi |
| 2021-09-20 | Remove proof-of-concept test code...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Remove the proof-of-concept CLI-only module that was used to learn how the
heatmaps work and identify the appropriate data for use with them.
| Frederick Muriuki Muriithi |
| 2021-09-20 | Return only the data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Parse incoming data to build up correct trait names and
respond with only the computed heatmap data.
* gn3/heatmaps.py: Return only the computed data for heatmaps and clustering.
Since GN3 is supposed to handle only the data, and db-access, this commit
ensures that GN3 responds to the client with only the computed heatmap data,
and does not try to generate the heatmaps themselves.
The generation of the heatmaps will be delegated to the UI clients, such as
GeneNetwork2.
| Frederick Muriuki Muriithi |
| 2021-09-17 | Fix a number of linting issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Frederick Muriuki Muriithi |
| 2021-09-17 | Return path to generated filename for now...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* To help with demonstrating that the code is producing the expected output,
for now, we return the path to the generated html file that displays the
interactive heatmap.
At this point, it is mostly useful in the development environment. Moving
forward, we might have to actually stream the raw html, or if we can get the
Kaleido library packaged for GNU Guix, stream the images binary data instead.
| Frederick Muriuki Muriithi |
| 2021-09-17 | Fix some layout issues and update colorscale...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the plot layouts and size to display the dendrogram and individual
chromosome heatmaps side by side
* Update the colour scale to begin with the grays rather than absolute black
| Frederick Muriuki Muriithi |
| 2021-09-17 | Create dendrogram to show clustering tree...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the clustering data to be used for the creation of the clustering
dendrogram in the final clustered heatmap plot.
| Frederick Muriuki Muriithi |
| 2021-09-16 | pylint fixes | Alexander Kabui |
| 2021-09-16 | Add WGCNA_SCRIT env to settings | Alexander Kabui |
| 2021-09-16 | init tests for wgcna | Alexander Kabui |
| 2021-09-16 | pass user input to call script | Alexander Kabui |
| 2021-09-16 | Intergrate the heatmap generation with the API...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Intergrate the heatmap generation code on the /api/heatmaps/clustered
endpoint.
The endpoint should take a json query of the form:
{"traits_names": [ ... ] }
where the "traits_name" value is a list of the full names of traits.
A sample query to the endpoint could be something like the following:
curl -i -X POST "http://localhost:8080/api/heatmaps/clustered" \
-H "Accept: application/json" \
-H "Content-Type: application/json" \
-d '{
"traits_names": [
"UCLA_BXDBXH_CARTILAGE_V2::ILM103710672",
"UCLA_BXDBXH_CARTILAGE_V2::ILM2260338",
"UCLA_BXDBXH_CARTILAGE_V2::ILM3140576",
"UCLA_BXDBXH_CARTILAGE_V2::ILM5670577",
"UCLA_BXDBXH_CARTILAGE_V2::ILM2070121",
"UCLA_BXDBXH_CARTILAGE_V2::ILM103990541",
"UCLA_BXDBXH_CARTILAGE_V2::ILM1190722",
"UCLA_BXDBXH_CARTILAGE_V2::ILM6590722",
"UCLA_BXDBXH_CARTILAGE_V2::ILM4200064",
"UCLA_BXDBXH_CARTILAGE_V2::ILM3140463"
]
}'
which should respond with a json response containing the raw binary string
for the png format and possibly another for the svg format.
| Frederick Muriuki Muriithi |
| 2021-09-16 | Fix minor bugs...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix a few minor bugs left over from the integration of code from the
proof-of-concept code.
| Frederick Muriuki Muriithi |
| 2021-09-16 | Add missing imports...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add missing imports that are needed in the code.
| Frederick Muriuki Muriithi |
