Update uns[{column}_colors] to match ordering in implementation

[brian-mott]

Context

While curating a recent Collection, I ran into some ambiguity to wrangle column color information from the obs dataframe into uns[{column}_colors]. The readme notes that:

The color code at the Nth position in the ndarray corresponds to the Nth category of anndata.obs.{column}.unique()

anndata.obs.{column}.unique() will return an unsorted list of category names for {column} as they are encountered in the obs dataframe.

It looks like this line in the single_cell_data_portal repo assigns colors based on the adata.obs[column].cat.categories attribute, which returns a sorted list of the category names.

Once I realized this, it was easy to map colors in the proper order after sorting or using adata.obs[column].cat.categories but I think it would be helpful to have some further clarity explaining that the uns[{column}_colors] array depends on the sorted order of category names.

Design (@brianraymor)

{column}_colors

Key	{column}_colors where {column} MUST be the name of a category data type column in obs that is annotated by the data submitter or curator. The following columns that are annotated by CELLxGENE Discover MUST NOT be specified as {column}: assay cell_type development_stage disease organism self_reported_ethnicity sex tissue Instead annotate {column}_ontology_term_id_colors for these columns such as assay_ontology_term_id.
Annotator	Curator MAY annotate.
Value	numpy.ndarray. This MUST be a 1-D array of shape (, c), where c is greater than or equal to the number of categories in the {column} as calculated by: anndata.obs.{column}.cat.categories.size The color code at the Nth position in the ndarray corresponds to the Nth category of anndata.obs.{column}.cat.categories. For example, if cell_type_ontology_term_id includes two categories: anndata.obs.cell_type_ontology_term_id.cat.categories.values array(['CL:0000057', 'CL:0000115'], dtype='object') then cell-type_ontology_term_id_colors MUST contain two or more colors such as: ['aqua' 'blueviolet'] where 'aqua' is the color assigned to 'CL:0000057' and 'blueviolet' is the color assigned to 'CL:0000115'. All elements in the ndarray MUST use the same color model, limited to: Color Model Element Format Named Colors str. MUST be a case-insensitive CSS4 color name with no spaces such as "aliceblue" Hex Triplet str. MUST start with "#" immediately followed by six case-insensitive hexadecimal characters as in "#08c0ff"

[brianraymor]

Hmm. The objective is that the implementation match the schema requirements; otherwise, it should not pass QA.

See an earlier comment thread where the difference between unique and cat.catgories was under discussion. And the same line of code was referenced.

CC: @niknak33 @atarashansky

[brianraymor]

April 25 - per review with @dsadgat and recommendation by @jahilton, the schema to be updated to match the current CXG implementation. It will specify cat.categories instead of unique().