| Age | Commit message (Expand) | Author |
|---|
| 2021-08-27 | Export trait data to file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide a function to export the given strains and traits data into a traits
file for use with `rust-qtlreaper`.
| Muriithi Frederick Muriuki |
| 2021-08-27 | Rework strains and trait values retrieval...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Rework the strains and values retrieval function to more closely correspond
to the working of the original code in GN1
| Muriithi Frederick Muriuki |
| 2021-08-20 | Fix typing issue(s) caught by mypy...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Use `Sequence` type not `Iterator` type
| Muriithi Frederick Muriuki |
| 2021-08-20 | Retrieve the strains with valid values...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: add function to get strains with values
* tests/unit/computations/test_heatmap.py: new tests
Add function to get the strains whose values are not `None` from the
`trait_data` object passed in.
This migrates
https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221
into a separate function that can handle that and be tested independently of
any other code.
| Muriithi Frederick Muriuki |
| 2021-08-20 | Add tests for ordering and implement function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: implement new ordering function
* tests/unit/computations/test_heatmap.py: add new tests
Implement the ordering function to migrate the setup of the `neworder`
variable from GN1 to GN3.
This migration is incomplete, since there is dependence on the return from
the `web.webqtl.heatmap.Heatmap.draw` function in form of the `d_1` variable
in some of the paths.
The thing is, this `d_1` variable, and the `xoffset` variable seem to be
used for laying out things on the drawn heatmap, and might actually end up
not being needed for the new system using plotly, which has other ways of
laying out things on the drawing.
For now though, this commit "shims" the presence of these values until when
the use of these variables is confirmed as present or absent in the new GN3
system.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Test the clustering...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix clustering bugs
* tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues.
Test and fix the clustering function.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Add tests and fix errors caught with tests...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: fix errors
* tests/unit/computations/test_heatmap.py: new tests
Add new tests with the expected source data format, and expected results.
Fix all errors that were caught by running the tests
| Muriithi Frederick Muriuki |
| 2021-08-12 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix some errors caught by the linter.
| Muriithi Frederick Muriuki |
| 2021-08-12 | Import missing definitions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Import some missing definitions.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Build up the heatmap data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add code to compute and organise the data that will be used to draw the
final heatmap.
This varies significantly in how it works from the original, but it still
tries to retain the general flow of data.
| Muriithi Frederick Muriuki |
