| Age | Commit message (Collapse) | Author |
|---|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The heatmap generation does not fall cleanly within the computations or db
modules. This commit moves it to the higher level gn3 module.
|
|
* tests/unit/computations/test_heatmap.py: ordering is not longer provided as
a list of tuples; the ordering values are just a list of numbers now. This
commit updates the test to take this into consideration.
* tests/unit/computations/test_qtlreaper.py: the 'Chr' value if numeric, is
represented by an actual number, not a string. This commit updates the code
to take this into consideration.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix ordering function
* tests/unit/computations/test_heatmap.py: update test
The order of the traits is important for the clustering algorithm, since the
clustering seems to use the distance of one trait from another to determine
how to order them.
This commit also gets rid of the xoffset argument that is not important to
the ordering, and was used in the older GN1 to determine how to draw the
clustering lines.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The number of the arguments to the function changed, and so the tests for
the function needed to be updated.
|
|
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.
|
|
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.
|
|
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.
|
|
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
|
