more name fixes, example notebook corrected for names

Author: lee-t

bioplexpy/analysis_funcs.py

@@ -150,8 +150,8 @@ def get_PPI_network_for_complex(bp_PPI_G, Corum_DF, Complex_ID):
     12
     '''
     # store gene UNIPROT IDs that belong to this complex in a list
-    genes_in_complex_i = (Corum_DF[Corum_DF.ComplexID == Complex_ID].loc[:,
-                                'subunits(UniProt IDs)'].values[0].split(';'))
+    genes_in_complex_i = (Corum_DF[Corum_DF.complex_id == Complex_ID].loc[:,
+                                'subunits_uniprot_id'].values[0].split(';'))
 
     # get subgraph induced by the subset of nodes in this CORUM complex
     bp_complex_i_G = bp_PPI_G.subgraph(genes_in_complex_i)
@@ -273,8 +273,8 @@ def get_prop_edges_in_complex_identified(bp_PPI_G, Corum_DF, Complex_ID):
     >>> get_prop_edges_in_complex_identified(bp_293t_G, Corum_DF, 2851)
     '''
     # store gene UNIPROT IDs that belong to this complex in a list
-    genes_in_complex_i = (Corum_DF[Corum_DF.ComplexID == Complex_ID].loc[:,
-                                'subunits(UniProt IDs)'].values[0].split(';'))
+    genes_in_complex_i = (Corum_DF[Corum_DF.complex_id == Complex_ID].loc[:,
+                                'subunits_uniprot_id'].values[0].split(';'))
 
     # get subgraph induced by the subset of nodes in this CORUM complex
     bp_complex_i_G = bp_PPI_G.subgraph(genes_in_complex_i)

bioplexpy/data_import_funcs.py

@@ -192,7 +192,7 @@ def getCorum(complex_set = 'all', organism = 'Human'):
 
 def get_UniProts_from_CORUM(Corum_DF, Complex_ID):
     '''
-    Retreive set of UniProt IDs corresponding to a CORUM complex ID.
+    Retrieve set of UniProt IDs corresponding to a CORUM complex ID.
     
     This function takes a CORUM complex ID and CORUM complex DataFrame
     and returns the corresponding UniProt IDs.
@@ -293,7 +293,7 @@ def get_PDB_from_UniProts(uniprot_IDs_list):
             PDB_IDs_for_uniprot_dict[uniprot_ID_i] = mapped_PDB_ID_i
 
         else:
-            print(f'WARNING: {uniprot_ID_i_complex_i} does not have any '
+            print(f'WARNING: {uniprot_ID_i} does not have any '
                   'corresponding PDB IDs mapped.')
 
     # create dictionary of PDB IDs and store list of 

bioplexpy/visualization_funcs.py

@@ -52,12 +52,12 @@ def display_PPI_network_for_complex(ax, bp_PPI_df, Corum_DF, Complex_ID,
     {'A0A024R3R1': array([ 1.00000000e+00, -2.29248628e-09]), 'O75446': array([0.88545603, 0.46472316]), 'P29374': array([0.56806476, 0.82298384]), 'Q09028': array([0.12053671, 0.99270884]), 'Q13547': array([-0.35460481,  0.93501625]), 'Q16576': array([-0.74851068,  0.66312264]), 'Q5PSV4': array([-0.9709418 ,  0.23931567]), 'Q92769': array([-0.9709418 , -0.23931561]), 'Q96ST3': array([-0.7485108 , -0.66312258]), 'Q9H0E3': array([-0.35460499, -0.9350162 ]), 'Q9H160': array([ 0.12053676, -0.99270884]), 'Q9H7L9': array([ 0.56806458, -0.82298396]), 'Q9HCU9': array([ 0.88545603, -0.46472319])}
     '''
     # store uniprot IDs & gene symbols that belong to this complex in a list
-    genes_in_complex_i = (Corum_DF[Corum_DF.ComplexID == Complex_ID]
-                            .loc[:,'subunits(UniProt IDs)'].values[0]
+    genes_in_complex_i = (Corum_DF[Corum_DF.complex_id == Complex_ID]
+                            .loc[:,'subunits_uniprot_id'].values[0]
                             .split(';')) # Uniprot
 
-    gene_symbols_in_complex_i = (Corum_DF[Corum_DF.ComplexID == Complex_ID]
-                                 .loc[:,'subunits(Gene name)'].values[0]
+    gene_symbols_in_complex_i = (Corum_DF[Corum_DF.complex_id == Complex_ID]
+                                 .loc[:,'subunits_gene_name'].values[0]
                                  .split(';')) # Symbol
 
     # filter BioPlex PPI dataframe to include only interactions