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Support diffmap and phate layouts. Explicitly handle embeddings with >2 components. (#662)

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* Add diffmap and phate to supported embeddings

* Explicitly pull the first two components of any given layout
This commit is contained in:
Sidney Bell
2019-03-21 19:06:05 -07:00
committed by GitHub
parent 016a4a422a
commit 16f93397ae
3 changed files with 8 additions and 3 deletions
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server/app/scanpy_engine/scanpy_engine.py
+6 -1
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@@ -328,10 +328,15 @@ class ScanpyEngine(CXGDriver):
* only returns Matrix in columnar layout
"""
try:
df_layout = self.data.obsm[f"X_{self.layout_method}"]
full_embedding = self.data.obsm[f"X_{self.layout_method}"]
if full_embedding.shape[1] > 2:
warnings.warn(f"Warning: found {full_embedding.shape[1]} \
components of embedding. Using the first two for layout display.")
df_layout = full_embedding[:, :2]
except ValueError as e:
raise PrepareError(
f"Layout has not been calculated using {self.layout_method}, "
f"please prepare your datafile and relaunch cellxgene") from e
normalized_layout = (df_layout - df_layout.min()) / (df_layout.max() - df_layout.min())
return encode_matrix_fbs(normalized_layout.astype(dtype=np.float32), col_idx=None, row_idx=None)