NickAkhmetov/Add support for obs_labels_names and obs_labels_paths arrays

tests/create_test_data.py

@@ -139,10 +139,11 @@ def create_test_anndata_file(h5ad_path):
  'exPFC2',
  'GABA2'
  ]
+ obs_cell_label_arr = [f'{obs_label}-label' for obs_label in obs_celltype_arr]
  obs_df = pd.DataFrame(
  data=[
- {'index': i, 'CellType': ct}
- for i, ct in zip(obs_index_arr, obs_celltype_arr)
+ {'index': i, 'CellType': ct, 'CellLabel': cl}
+ for i, ct, cl in zip(obs_index_arr, obs_celltype_arr, obs_cell_label_arr)
  ]
  )
  obsm = {"X_umap": np.array([[0, 1] for c in obs_index_arr])}

tests/test_wrappers.py

@@ -141,16 +141,19 @@ def test_ome_zarr_with_base_dir(self):
 
  def test_anndata(self):
  adata_path = data_path / 'test.h5ad.zarr'
- w = AnnDataWrapper(adata_path, obs_set_paths=['obs/CellType'], obs_set_names=['Cell Type'], obs_embedding_paths=[
- 'obsm/X_umap'], obs_embedding_names=['UMAP'])
+ w = AnnDataWrapper(adata_path,
+ obs_set_paths=['obs/CellType'], obs_set_names=['Cell Type'],
+ obs_labels_names=['Cell Label'], obs_labels_paths=['obs/CellLabel'],
+ obs_embedding_paths=['obsm/X_umap'], obs_embedding_names=['UMAP'])
  w.local_dir_uid = 'anndata.zarr'
 
  file_def_creator = w.make_file_def_creator('A', 0)
  file_def = file_def_creator('http://localhost:8000')
  self.assertEqual(file_def, {'fileType': 'anndata.zarr', 'url': 'http://localhost:8000/A/0/anndata.zarr',
  'options': {
  'obsEmbedding': [{'path': 'obsm/X_umap', 'embeddingType': 'UMAP', 'dims': [0, 1]}],
- 'obsSets': [{'path': 'obs/CellType', 'name': 'Cell Type'}]
+ 'obsSets': [{'path': 'obs/CellType', 'name': 'Cell Type'}],
+ 'obsLabels': [{'path': 'obs/CellLabel', 'obsLabelsType': 'Cell Label'}]
  }})
 
  def test_anndata_with_base_dir(self):

vitessce/wrappers.py

@@ -506,7 +506,7 @@ def create_image_json(self, img_url):
 
 
 class AnnDataWrapper(AbstractWrapper):
- def __init__(self, adata_path=None, adata_url=None, obs_feature_matrix_path=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, request_init=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, **kwargs):
+ def __init__(self, adata_path=None, adata_url=None, obs_feature_matrix_path=None, feature_filter_path=None, initial_feature_filter_path=None, obs_set_paths=None, obs_set_names=None, obs_locations_path=None, obs_segmentations_path=None, obs_embedding_paths=None, obs_embedding_names=None, obs_embedding_dims=None, request_init=None, feature_labels_path=None, obs_labels_path=None, convert_to_dense=True, coordination_values=None, obs_labels_paths=None, obs_labels_names=None, **kwargs):
  """
  Wrap an AnnData object by creating an instance of the ``AnnDataWrapper`` class.
 
@@ -516,15 +516,17 @@ def __init__(self, adata_path=None, adata_url=None, obs_feature_matrix_path=None
  :param str feature_filter_path: A string like `var/highly_variable` used in conjunction with `obs_feature_matrix_path` if obs_feature_matrix_path points to a subset of `X` of the full `var` list.
  :param str initial_feature_filter_path: A string like `var/highly_variable` used in conjunction with `obs_feature_matrix_path` if obs_feature_matrix_path points to a subset of `X` of the full `var` list.
  :param list[str] obs_set_paths: Column names like `['obs/louvain', 'obs/cellType']` for showing cell sets
- :param list[str] obs_set_names: Names to display in place of those in `obs_set_paths`, like `['Louvain', 'Cell Type']
+ :param list[str] obs_set_names: Names to display in place of those in `obs_set_paths`, like `['Louvain', 'Cell Type']`
  :param str obs_locations_path: Column name in `obsm` that contains centroid coordinates for displaying centroids in the spatial viewer
  :param str obs_segmentations_path: Column name in `obsm` that contains polygonal coordinates for displaying outlines in the spatial viewer
  :param list[str] obs_embedding_paths: Column names like `['obsm/X_umap', 'obsm/X_pca']` for showing scatterplots
- :param list[str] obs_embedding_names: Overriding names like `['UMAP', 'PCA'] for displaying above scatterplots
- :param list[str] obs_embedding_dims: Dimensions along which to get data for the scatterplot, like [[0, 1], [4, 5]] where [0, 1] is just the normal x and y but [4, 5] could be comparing the third and fourth principal components, for example.
- :param dict request_init: options to be passed along with every fetch request from the browser, like { "header": { "Authorization": "Bearer dsfjalsdfa1431" } }
+ :param list[str] obs_embedding_names: Overriding names like `['UMAP', 'PCA']` for displaying above scatterplots
+ :param list[str] obs_embedding_dims: Dimensions along which to get data for the scatterplot, like `[[0, 1], [4, 5]]` where `[0, 1]` is just the normal x and y but `[4, 5]` could be comparing the third and fourth principal components, for example.
+ :param dict request_init: options to be passed along with every fetch request from the browser, like `{ "header": { "Authorization": "Bearer dsfjalsdfa1431" } }`
  :param str feature_labels_path: The name of a column containing feature labels (e.g., alternate gene symbols), instead of the default index in `var` of the AnnData store.
- :param str obs_labels_path: The name of a column containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
+ :param str obs_labels_path: (DEPRECATED) The name of a column containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store. Use `obs_labels_paths` and `obs_labels_names` instead. This arg will be removed in a future release.
+ :param list[str] obs_labels_paths: The names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
+ :param list[str] obs_labels_names: The optional display names of columns containing observation labels (e.g., alternate cell IDs), instead of the default index in `obs` of the AnnData store.
  :param bool convert_to_dense: Whether or not to convert `X` to dense the zarr store (dense is faster but takes more disk space).
  :param coordination_values: Coordination values for the file definition.
  :type coordination_values: dict or None
@@ -559,7 +561,13 @@ def __init__(self, adata_path=None, adata_url=None, obs_feature_matrix_path=None
  self._mappings_obsm_dims = obs_embedding_dims
  self._request_init = request_init
  self._gene_alias = feature_labels_path
- self._obs_labels_path = obs_labels_path
+ # Support legacy provision of single obs labels path
+ if (obs_labels_path is not None):
+ self._obs_labels_paths = [obs_labels_path]
+ self._obs_labels_names = [obs_labels_path.split('/')[-1]]
+ else:
+ self._obs_labels_paths = obs_labels_paths
+ self._obs_labels_names = obs_labels_names
  self._convert_to_dense = convert_to_dense
  self._coordination_values = coordination_values
 
@@ -642,10 +650,18 @@ def get_anndata_zarr(base_url):
  options["featureLabels"] = {
  "path": self._gene_alias
  }
- if self._obs_labels_path is not None:
- options["obsLabels"] = {
- "path": self._obs_labels_path
- }
+ if self._obs_labels_paths is not None:
+ if self._obs_labels_names is not None and len(self._obs_labels_paths) == len(self._obs_labels_names):
+ # A name was provided for each path element, so use those values.
+ names = self._obs_labels_names
+ else:
+ # Names were not provided for each path element,
+ # so fall back to using the final part of each path for the names.
+ names = [labels_path.split('/')[-1] for labels_path in self._obs_labels_paths]
+ obs_labels = []
+ for path, name in zip(self._obs_labels_paths, names):
+ obs_labels.append({"path": path, "obsLabelsType": name})
+ options["obsLabels"] = obs_labels
  if len(options.keys()) > 0:
  obj_file_def = {
  "fileType": ft.ANNDATA_ZARR.value,