fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-06 20:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Remove cell ids from engine

Browse Source 
Previously I just removed them from the driver
This commit is contained in:
Charlotte Weaver
2018-07-06 15:38:42 -07:00
parent e3bf06ca61
commit 354eacc3c8
2 changed files with 5 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/app/rest_api/rest.py
+1 -3
View File
@@ -193,7 +193,6 @@ class CellsAPI(Resource):
def get(self): def get(self):
from app import data from app import data
payload = { payload = {
"cellids": [],
"metadata": [], "metadata": [],
"cellcount": 0, "cellcount": 0,
"graph": [], "graph": [],
@@ -205,8 +204,7 @@ class CellsAPI(Resource):
payload["metadata"] = data.metadata(filtered_data) payload["metadata"] = data.metadata(filtered_data)
payload["ranges"] = data.metadata_ranges(filtered_data) payload["ranges"] = data.metadata_ranges(filtered_data)
payload["graph"] = data.create_graph(filtered_data) payload["graph"] = data.create_graph(filtered_data)
payload["cellids"] = data.cellids(filtered_data) payload["cellcount"] = data.cell_count
payload["cellcount"] = len(payload["cellids"])
return make_payload(payload) return make_payload(payload)
server/app/scanpy_engine/scanpy_engine.py
+4 -12
View File
@@ -13,12 +13,15 @@ class ScanpyEngine(CXGDriver):
def __init__(self, data, schema=None, graph_method="umap", diffexp_method="ttest"): def __init__(self, data, schema=None, graph_method="umap", diffexp_method="ttest"):
self.data = self._load_data(data) self.data = self._load_data(data)
self.schema = self._load_or_infer_schema(data, schema) self.schema = self._load_or_infer_schema(data, schema)
self._set_cell_ids() self._set_cell_names()
self.cell_count = self.data.shape[0] self.cell_count = self.data.shape[0]
self.gene_count = self.data.shape[1] self.gene_count = self.data.shape[1]
self.graph_method = graph_method self.graph_method = graph_method
self.diffexp_method = diffexp_method self.diffexp_method = diffexp_method
def _set_cell_names(self):
self.data.obs["cell_name"] = list(self.data.obs.index)
@staticmethod @staticmethod
def _load_data(data): def _load_data(data):
return sc.read(os.path.join(data, "data.h5ad")) return sc.read(os.path.join(data, "data.h5ad"))
@@ -32,20 +35,9 @@ class ScanpyEngine(CXGDriver):
data_schema = parse_schema(os.path.join(data, schema)) data_schema = parse_schema(os.path.join(data, schema))
return data_schema return data_schema
def _set_cell_ids(self):
self.data.obs["cxg_cell_id"] = list(range(self.data.obs.shape[0]))
self.data.obs["cell_name"] = list(self.data.obs.index)
self.data.obs.set_index("cxg_cell_id", inplace=True)
def cells(self): def cells(self):
return list(self.data.obs.index) return list(self.data.obs.index)
def cellids(self, df=None):
if df:
return list(df.obs.index)
else:
return list(self.data.obs.index)
def genes(self): def genes(self):
return self.data.var.index.tolist() return self.data.var.index.tolist()