MSCommunity visualization polishing

freiburgermsu · Jul 19, 2023 · 8bb7300 · 8bb7300
1 parent 24f1939
commit 8bb7300
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/modelseedpy/community/mscommscores.py b/modelseedpy/community/mscommscores.py
@@ -328,15 +328,15 @@ def calculate_scores(pairs, models_media=None, environments=None, RAST_genomes=N
                             del kbase_dic[f"MIP_model{modelIDs.index(models_name)+1}"]
                         if print_progress:  print("costless_MIP  done", end="\t")
                     if print_progress:  print("MIP done", end="\t")
-                    kbase_dic.update({"PC": f"{MSCommScores.pc(grouping, comm_model, comm_sol, community=community)[0]:.5f}"})
-                    if print_progress:  print("PC  done", end="\t")
                     bss_values = MSCommScores.bss(None, [model_utils[model1.id], model_utils[model2.id]],
                                                   environments, models_media, anme_comm)
                     kbase_dic.update({f"BSS_model{modelIDs.index(name.split(' invading ')[0])+1}": f"{val:.5f}"
                                       for name, val in bss_values.items()})
                     if print_progress:  print("BSS done", end="\t")
                     kbase_dic.update({"BIT": MSCommScores.bit(grouping, comm_model, comm_sol=comm_sol, community=community)})
                     if print_progress:  print("BIT done", end="\t")
+                    kbase_dic.update({"PC": f"{MSCommScores.pc(grouping, comm_model, comm_sol, community=community)[0]:.5f}"})
+                    if print_progress:  print("PC  done", end="\t")
                     # determine the growth diff content
                     kbase_dic.update({"GYD": f"""{list(MSCommScores.gyd(
                         grouping, environment=environ, community=community, anme_comm=anme_comm).values())[0]:.5f}"""})

diff --git a/modelseedpy/community/mssteadycom.py b/modelseedpy/community/mssteadycom.py
@@ -235,7 +235,8 @@ def visual_interactions(cross_feeding_df, filename="cross_feeding", export_forma
         metabolites_df = concat(cross_feeding_rows, axis=1).T
         metabolites_df.index.name = "Metabolite ID"
         display(metabolites_df)
-        metabolites = [msdb.compounds.get_by_id(metID.replace("_e0", "")) for metID in metabolites_df.index.tolist()]
+        metabolites = [msdb.compounds.get_by_id(metID.replace("_e0", "")) for metID in metabolites_df.index.tolist()
+                       if metID not in ["cpdETCM", "cpdETCMe"]]
         # define the community members that participate in cross-feeding
         members = metabolites_df.loc[:, (metabolites_df != 0).any(axis=0)].columns.tolist()
         members.remove("Environment")
@@ -268,12 +269,13 @@ def visual_interactions(cross_feeding_df, filename="cross_feeding", export_forma
         # define the edges by parsing the interaction DataFrame
         for met in metabolites:
             row = metabolites_df.loc[met.id]
+            maxVal = max(list(row.to_numpy()))
             for col, val in row.items():
                 if col == "Environment":  continue
                 index = members.index(col)
                 # TODO color carbon sources red
-                if val > 0:  dot.edge(f"S{index}", met.abbr[:3], arrowsize=f"{val / 500}", edgetooltip=str(val))
-                if val < 0:  dot.edge(met.abbr[:3], f"S{index}", arrowsize=f"{abs(val / 500)}", edgetooltip=str(val))
+                if val > 0:  dot.edge(f"S{index}", met.abbr[:3], arrowsize=f"{val / maxVal}", edgetooltip=str(val))
+                if val < 0:  dot.edge(met.abbr[:3], f"S{index}", arrowsize=f"{abs(val / maxVal)}", edgetooltip=str(val))
 
         # render and export the source
         dot.render(filename, view=view_figure)