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feat(plots): plot inferred time-clonal fate potency correlation #647

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feat(plots): plot inferred time-clonal fate potency correlation #647

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@cameronraysmith cameronraysmith commented Aug 23, 2024 •
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fix(plots): use vector field basis in shared time uncertainty plot
4fb202b 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith added the skip-ci Skip CI workflow label Aug 23, 2024
@cameronraysmith cameronraysmith self-assigned this Aug 23, 2024
@cameronraysmith cameronraysmith added this to the 0.4.x milestone Aug 23, 2024
@cameronraysmith
fix(utils): add array-based type class aliases
81aef5d 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(utils): remove unused comments
9292cdd 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(utils): include size and category information in data string rep…
04b8e7d 
…resentation

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith added skip-ci Skip CI workflow enhancement New feature or request python Pull requests that update Python code and removed skip-ci Skip CI workflow labels Aug 23, 2024
@cameronraysmith
feat(plots): draft lineage fate correlation plot
ee3ae34 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
refactor(plots): rename vector field uncertainty plot function
8fc0d94 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): enable type-checking of plot lineage fate correlation
4843c4b 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): export lineage fate correlation plot from plots package
601e0c8 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(io): serialize np.bool_ to bool
86e54f0 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
refactor(tasks): migrate data subset functionality to io package
3d1316c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith linked an issue Aug 24, 2024 that may be closed by this pull request
add plots module for cell fate metrics comparison #621
Open
@cameronraysmith
refactor(tasks): move load data function to utils
0adac20 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(utils): add function to compute file hashes
7ede4bc 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): type-check get clone trajectory function
7f438b3 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): use pandas regex str replacement in lineage fate correlation
34cfd15 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
refactor(plots): archive unused code from get clone trajectory
b7eadc4 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(styles): add module for explicit specification of colors
7622639 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): parameterize posterior time color map
155a131 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
nit(plots): update comments
81c5edf 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): include time and angle uncertainty
f45f308 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(tasks): draft time fate correlation task
d07e961 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): disable transparency in lineage fate correlation
ff63d31 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): remove unused comment from posterior predictive extrapola…
44cd705 
…tion

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): remove additional unused comments from posterior predicti…
8174ff9 
…ve extrapolation

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): update mae_per_gene function and add docstring
0ac2cdf 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): remove unused comments from compute_volcano_data
d62db2f 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): optionally force recomputation of volcano data
c2ede44 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(plots): parameterize inclusion of complete angular scale
f31d116 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): add shadow support for jax arrays
46ad2b5 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(analysis): add basic tests for mae_per_gene
40a0125 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(tests): add function to generate fixture data
3986cd4 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(tests): test ability to load and log data string diff with seria…
a7ec817 
…lized

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): add serialization test for uns dict with nested numpy array
6d376d9 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(tests): add preprocessed pancreas 50x13 fixture data
0c71a68 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(io): add debug logging of attempted serialization dictionary to s…
7910665 
…erialize anndata

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tasks): add soft support for selected genes to preprocessing
d3227ac 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(io): restore types when deserializing json
ea08a4a 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): note handling of selected genes in generate fixture data
351bc17 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): add unprocessed data fixture
d520dcc 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): add processed data fixture
24e8d28 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
wip(tests): sketch smoke test execution of VelocityModule
6ec2b0c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): rename small deserialized data fixture in plots
a096c8c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): load preprocessed deserialized data fixture globally
8752319 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(interfaces): add default factory for preprocess selected_genes em…
be70f2c 
…pty list

resolves

```
ValueError: mutable default <class 'list'> for field selected_genes is not allowed: use default_factory
```

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(io): optionally check file hashes when (de)serializing json files
0b63cc6 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(io): update serialization tests with expectation specs
f03454d 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): update fixture name for preprocessed_3_4 in plot histograms
4198735 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(tests): exercise hash check in data serialization
9163a92 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(tests): add function to generate postprocessed fixture data
793a72e 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(train): add unit test for train task on static fixture data
f96a775 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
tests(data): add trained pancreas 50 by 7 fixture
847bbc9 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
tests(data): add postprocessed pancreas 50 by 7 fixture
5baa10a 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
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