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/cells is working

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This commit is contained in:
Charlotte Weaver
2018-06-22 11:52:05 -07:00
parent 9b4bcb7f7b
commit ee8bb510ff
2 changed files with 17 additions and 25 deletions
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6
backend/app/rest_api/rest.py
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@@ -202,11 +202,11 @@ class CellsAPI(Resource):
# get query params
filter = parse_filter(request.args, data.schema)
filtered_data = data.filter_cells(filter)
payload["metadata"] = list(data.metadata(filtered_data))
payload["metadata"] = data.metadata(filtered_data)
payload["ranges"] = data.metadata_ranges(filtered_data)
payload["cellids"] = filtered_data
payload["graph"] = data.create_graph(filtered_data)
payload["cellids"] = data.cellids(filtered_data)
payload["cellcount"] = len(payload["cellids"])
payload["graph"] = list(data.create_graph(filtered_data))
return make_payload(payload)

36
backend/app/scanpy_engine/scanpy_engine.py
View File

@@ -40,12 +40,11 @@ class ScanpyEngine(CXGDriver):
def cells(self):
return list(self.data.obs.index)
def cellids(self, cells_iterator=None):
if cells_iterator:
data = self.data.obs.iloc[[i for i in cells_iterator], :]
def cellids(self, df=None):
if df:
return list(df.obs.index)
else:
data = self.data.obs
return list(data.index)
return list(self.data.obs.index)
def genes(self):
return self.data.var.index.tolist()
@@ -56,7 +55,7 @@ class ScanpyEngine(CXGDriver):
:param filter:
:return: iterator through cell ids
"""
cell_idx = np.ones((self.cell_count(),), dtype=bool)
cell_idx = np.ones((self.cell_count,), dtype=bool)
for key, value in filter.items():
if value["variable_type"] == "categorical":
key_idx = np.in1d(getattr(self.data.obs, key), value["query"])
@@ -91,33 +90,26 @@ class ScanpyEngine(CXGDriver):
}
return metadata_ranges
def metadata(self, cells_iterator, fields=None):
def metadata(self, df, fields=None):
"""
Generator for metadata. Gets the metadata values cell by cell and returns all value
or only certain values if names is not None
:param cells_iterator: from filter cells, iterator for cellids
:param fields: list of keys for metadata to return, returns all metadata values if not set.
:return: Iterator for cellid + list of cells metadata values ex. [cell-id, val1, val2, val3]
"""
if not fields:
fields = self.data.obs.columns.tolist()
for cell_id in cells_iterator:
yield [cell_id] + self.data.obs.loc[cell_id, fields].tolist()
metadata = df.obs.to_dict(orient="records")
for idx in range(len(metadata)):
metadata[idx]["CellName"] = metadata[idx].pop("cell_name", None)
return metadata
def create_graph(self, cells_iterator):
def create_graph(self, df):
"""
Computes a n-d layout for cells through dimensionality reduction.
:param cells_iterator: from filter cells, iterator for cellids
:return: Iterator for [cellid-1, pos1, pos2], [cellid-2, pos1, pos2]
"""
cell_ids = list(cells_iterator)
getattr(sc.tl, self.graph_method)(self.data[self.data.obs.index.isin(cell_ids)])
graph = self.data.obsm["X_{graph_method}".format(graph_method=self.graph_method)]
getattr(sc.tl, self.graph_method)(df)
graph = df.obsm["X_{graph_method}".format(graph_method=self.graph_method)]
normalized_graph = (graph - graph.min()) / (graph.max() - graph.min())
for idx, cell_id in enumerate(cell_ids):
yield [cell_id] + normalized_graph[idx].tolist()
return np.hstack((df.obs["cell_name"].values.reshape(len(df.obs.index), 1), normalized_graph)).tolist()
def diffexp(self, cells_iterator_1, cells_iterator_2):