expfeat: implement anndata transform adaptor (#341)

* expfeat: implement anndata transform adaptor

* hotfix: fix anndata adaptor and cell feat graph

---------

Co-authored-by: Wenzhuo Tang <tangwen2@msu.edu>

dance/transforms/base.py

@@ -1,6 +1,9 @@
 import hashlib
+import warnings
 from abc import ABC, abstractmethod
 
+from anndata import AnnData
+
 from dance import logger
 from dance.data.base import Data
 from dance.typing import LogLevel, Optional, Tuple
@@ -44,3 +47,30 @@ def __repr__(self) -> str:
  @abstractmethod
  def __call__(self, data: Data) -> Data:
  raise NotImplementedError
+
+
+class AnnDataAdaptor:
+ """Adaptor for transforming AnnData instead of dance data object.
+
+ Example
+ -------
+ Modify an :class:`AnnData` object inplace
+
+ >>> AnnDataAdaptor(FilterGenes(mode="sum"))(adata)
+
+ """
+
+ def __init__(self, transform, **data_init_kwargs):
+ warnings.warn(
+ "This is a temporary patch to enable transforming AnnData, and "
+ "might have potential incompatibility issues. Use cautiously.",
+ UserWarning,
+ stacklevel=2,
+ )
+ self.transform = transform
+ self.data_init_kwargs = data_init_kwargs
+
+ def __call__(self, adata: AnnData) -> AnnData:
+ data = Data(adata, **self.data_init_kwargs)
+ self.transform(data)
+ return data.data

dance/transforms/graph/cell_feature_graph.py

@@ -34,7 +34,7 @@ def __call__(self, data):
  num_cells, num_feats = feat.shape
 
  row, col = np.nonzero(feat)
- edata = np.array(feat[row, col])[:, None]
+ edata = np.array(feat[row, col]).ravel()[:, None]
  self.logger.info(f"Number of nonzero entries: {edata.size:,}")
  self.logger.info(f"Nonzero rate = {edata.size / num_cells / num_feats:.1%}")