if args.superstages is not None:
superstage_dict = IOutils.parseStrToDict(args.superstages,
valueType="str",
pairSep=";")
try:
superstage_dict = OrderedDict([(k, [int(x) for x in v.split(",")])
for k, v in superstage_dict.items()])
except:
superstage_dict = OrderedDict([
(k, [int(re.search(r'(\d+)$', x).group(1)) for x in v.split(",")])
for k, v in superstage_dict.items()
])
############################################################################################################
## Load data
cellData = IOutils.loadCellData(
OrderedDict([("expr", args.fi_expr), ("pcComps", args.fi_stageIDs)]))
cellData = pd.concat([
cellData.loc[:,
("expr", slice(None))], cellData.loc[:,
("rowData", "clust_ID")]
],
axis=1) ## Remove unnecessary columns
cells_allowed = IOutils.readListFromFile(args.cells)
print("Restricting to {:d} allowed cells".format(len(cells_allowed)))
cellData = cellData.loc[cells_allowed, :].copy()
############################################################################################################
## COMPUTE CORRELATION BY STAGE
if not args.noSingleStageCorr:
stages = sorted(cellData["rowData"].loc[:, "clust_ID"].unique(),
key=lambda x: int(x))
