Cleanup

lineage/figures/figure13.py

@@ -16,17 +16,15 @@
 num_states = 3
 hgf_tHMMobj_list = Analyze_list(GFs, num_states)[0]
 
-hgf_states_list = [tHMMobj.predict() for tHMMobj in hgf_tHMMobj_list]
-
 # assign the predicted states to each cell
 for idx, hgf_tHMMobj in enumerate(hgf_tHMMobj_list):
+    states = hgf_tHMMobj.predict()
+
     for lin_indx, lin in enumerate(hgf_tHMMobj.X):
-        lin.states = hgf_states_list[idx][lin_indx]
+        lin.states = states[idx][lin_indx]
 
 T_hgf = hgf_tHMMobj_list[0].estimate.T
 
-num_states = hgf_tHMMobj_list[0].num_states
-
 rcParams["font.sans-serif"] = "Arial"
 
 

lineage/figures/figureS17.py

@@ -8,12 +8,13 @@
 from ..Analyze import Analyze_list
 
 hgf_tHMMobj_list = Analyze_list(GFs, 3)[0]
-hgf_states_list = [tHMMobj.predict() for tHMMobj in hgf_tHMMobj_list]
 
 # assign the predicted states to each cell
 for idx, hgf_tHMMobj in enumerate(hgf_tHMMobj_list):
+    states = hgf_tHMMobj.predict()
+
     for lin_indx, lin in enumerate(hgf_tHMMobj.X):
-        lin.states = hgf_states_list[idx][lin_indx]
+        lin.states = states[idx][lin_indx]
 
 for thmm_obj in hgf_tHMMobj_list:
     thmm_obj.X = sort_lins(thmm_obj)

lineage/plotTree.py

@@ -82,7 +82,7 @@ def CladeRecursive(cell: CellVar, a: list, censor: bool, color: bool):
         return my_clade
 
 
-def plotLineage(lineage: LineageTree, axes, censor: bool=True, color: bool=True):
+def plotLineage(lineage: LineageTree, axes, censor: bool = True, color: bool = True):
     """
     Given a lineage of cells, uses the `CladeRecursive` function to plot the lineage.
     """
@@ -107,7 +107,9 @@ def plotLineage(lineage: LineageTree, axes, censor: bool=True, color: bool=True)
     return draw(c, axes=axes)
 
 
-def plotLineage_MCF10A(lineage: LineageTree, axes, censor: bool=True, color: bool=True):
+def plotLineage_MCF10A(
+    lineage: LineageTree, axes, censor: bool = True, color: bool = True
+):
     """
     Given a lineage of cells, uses the `CladeRecursive` function to plot the lineage.
     """