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Add user-defined category-label colors (#1402)

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* Add user-defined category-label colors

Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152

As described in https://github.com/chanzuckerberg/cellxgene/issues/1307

* Respond to feedback from @bkmartinjr in nodejs

* Respond to feedback from @bkmartinjr in python

* Add tests to the server module

* Autoformat python, run linter

* Make colors_get error handling specific

* Respond to feedback from @bkmartinjr

* Respond to feedback from @bkmartinjr

* Fix whitespace

* Fix python lint errrors

* Update documentation

* Add --disable-user-colors option to launch and cxgtool.py

* Fix python formatting

* Rename '--disable-user-colors' to '--disable-custom-colors'
This commit is contained in:
Matt Weiden
2020-04-26 22:52:57 -07:00
committed by GitHub
parent 3c191c3f93
commit 546e272a60
91 changed files with 801 additions and 271 deletions
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server/test/test_anndata_adaptor.py
+14 -23
View File
@@ -10,10 +10,11 @@ from parameterized import parameterized_class
import numpy as np
import pandas as pd
from server.data_anndata.anndata_adaptor import AnndataAdaptor
from server.common.errors import FilterError
from server.common.data_locator import DataLocator
from server.common.app_config import AppConfig
from server.common.errors import FilterError
from server.data_anndata.anndata_adaptor import AnndataAdaptor
from server.test import PROJECT_ROOT, app_config
from server.test.test_datasets.fixtures import pbmc3k_colors
"""
Test the anndata adaptor using the pbmc3k data set.
@@ -23,30 +24,17 @@ Test the anndata adaptor using the pbmc3k data set.
@parameterized_class(
("data_locator", "backed"),
[
("../example-dataset/pbmc3k.h5ad", False),
("test/test_datasets/pbmc3k-CSC-gz.h5ad", False),
("test/test_datasets/pbmc3k-CSR-gz.h5ad", False),
("../example-dataset/pbmc3k.h5ad", True),
("test/test_datasets/pbmc3k-CSC-gz.h5ad", True),
("test/test_datasets/pbmc3k-CSR-gz.h5ad", True),
(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", False),
(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSC-gz.h5ad", False),
(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSR-gz.h5ad", False),
(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", True),
(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSC-gz.h5ad", True),
(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-CSR-gz.h5ad", True),
],
)
class AdaptorTest(unittest.TestCase):
def setUp(self):
args = {
"embeddings__names": ["umap", "tsne", "pca"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
"adaptor__anndata_adaptor__backed": self.backed,
"single_dataset__datapath": self.data_locator,
"limits__diffexp_cellcount_max": None,
"limits__column_request_max": None,
}
config = AppConfig()
config.update(**args)
config.complete_config()
config = app_config(self.data_locator, self.backed)
self.data = AnndataAdaptor(DataLocator(self.data_locator), config)
def test_init(self):
@@ -92,6 +80,9 @@ class AdaptorTest(unittest.TestCase):
self.assertEqual(np.sum(self.data.data.var[self.data.get_schema()["annotations"]["var"]["index"]].isna()), 0)
self.assertEqual(np.sum(self.data.data.obs[self.data.get_schema()["annotations"]["obs"]["index"]].isna()), 0)
def test_get_colors(self):
self.assertEqual(self.data.get_colors(), pbmc3k_colors)
def test_get_schema(self):
with open(path.join(path.dirname(__file__), "schema.json")) as fh:
schema = json.load(fh)