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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_diffexp.py
+5 -3
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@@ -5,6 +5,8 @@ import server.compute.diffexp_cxg as diffexp_cxg
import server.compute.diffexp_generic as diffexp_generic
import numpy as np
from server.test import PROJECT_ROOT
class DiffExpTest(unittest.TestCase):
"""Tests the diffexp returns the expected results for one test case, using different
@@ -50,7 +52,7 @@ class DiffExpTest(unittest.TestCase):
def test_anndata_default(self):
"""Test an anndata adaptor with its default diffexp algorithm (diffexp_generic)"""
adaptor = self.load_dataset("../example-dataset/pbmc3k.h5ad")
adaptor = self.load_dataset(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
maskA = self.get_mask(adaptor, 1, 10)
maskB = self.get_mask(adaptor, 2, 10)
results = adaptor.compute_diffexp_ttest(maskA, maskB, 10)
@@ -58,7 +60,7 @@ class DiffExpTest(unittest.TestCase):
def test_cxg_default(self):
"""Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg)"""
adaptor = self.load_dataset("test/test_datasets/pbmc3k.cxg")
adaptor = self.load_dataset(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg")
maskA = self.get_mask(adaptor, 1, 10)
maskB = self.get_mask(adaptor, 2, 10)
@@ -72,7 +74,7 @@ class DiffExpTest(unittest.TestCase):
def test_cxg_generic(self):
"""Test a cxg adaptor with the generic adaptor"""
adaptor = self.load_dataset("test/test_datasets/pbmc3k.cxg")
adaptor = self.load_dataset(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg")
maskA = self.get_mask(adaptor, 1, 10)
maskB = self.get_mask(adaptor, 2, 10)
# run it directly