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Format loaded dataset

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- create cell and gene ids
- recast numbers to float32/int32
This commit is contained in:
Charlotte Weaver
2018-08-09 11:23:43 -07:00
parent 3961bdc46d
commit 58000c1815
1 changed files with 19 additions and 0 deletions
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server/app/scanpy_engine/scanpy_engine.py
+19
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@@ -13,6 +13,7 @@ class ScanpyEngine(CXGDriver):
def __init__(self, data, schema=None, graph_method="umap", diffexp_method="ttest"):
self.data = self._load_data(data)
self._format_data()
self.schema = self._load_or_infer_schema(data, schema)
self._set_cell_names()
self.cell_count = self.data.shape[0]
@@ -39,6 +40,7 @@ class ScanpyEngine(CXGDriver):
def _load_data(data):
return sc.read(os.path.join(data, "data.h5ad"))
# TODO delete after v0.1 v2.0 transition
def _load_or_infer_schema(self, data, schema):
if not os.path.isfile(os.path.join(data, schema)):
# Initialize with cell name which is built off the index
@@ -75,6 +77,23 @@ class ScanpyEngine(CXGDriver):
data_schema = parse_schema(os.path.join(data, schema))
return data_schema
def _format_data(self):
# ensure gene
self.data.var["name"] = list(self.data.var.index)
self.data.var.index = list(range(self.data.var.shape[0]))
# ensure cell name
self.data.obs["name"] = list(self.data.obs.index)
self.data.obs.index = list(range(self.data.obs.shape[0]))
# ensure formats correct/ reform old format
for annotation in self.data.obs:
data_type = self.data.obs[annotation].dtype
if data_type.kind == 'f' and data_type != "float32":
self.data.obs[annotation] = self.data.obs[annotation].astype("float32")
elif data_type.kind in ['i', 'u'] and data_type != "int32":
self.data.obs[annotation] = self.data.obs[annotation].astype("int32")
if self.data.X.dtype != 'float32':
self.data.X = self.data.X.astype("float32")
def cells(self):
return list(self.data.obs.index)