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