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

* 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
+4
View File
@@ -12,6 +12,7 @@ from server_timing import Timing as ServerTiming
from server.data_common.data_adaptor import DataAdaptor
from server.data_common.fbs.matrix import encode_matrix_fbs
from server.common.utils import series_to_schema
from server.common.colors import convert_anndata_category_colors_to_cxg_category_colors
from server.common.constants import Axis, MAX_LAYOUTS
from server.common.errors import PrepareError, DatasetAccessError, FilterError
from server.compute.scanpy import scanpy_umap
@@ -333,6 +334,9 @@ class AnndataAdaptor(DataAdaptor):
lfc_cutoff = self.config.diffexp__lfc_cutoff
return diffexp_generic.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
def get_colors(self):
return convert_anndata_category_colors_to_cxg_category_colors(self.data)
def get_X_array(self, obs_mask=None, var_mask=None):
if obs_mask is None:
obs_mask = slice(None)