fix: correct minor mistake in pivot table generation for genomic anal…

…ysis.
ntorresd · Apr 24, 2023 · e812c7c · e812c7c
1 parent 16c256c
commit e812c7c
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/genomics/scripts/process_data.py b/genomics/scripts/process_data.py
@@ -25,7 +25,7 @@
 table = df_var.pivot(index='y_week',columns='lineage',values='n_seq_var')
 table.fillna(0, inplace = True)
 table = table.reset_index().reset_index().rename(columns = {'index':'t'}).reset_index(drop=True)
-del(table['y_week'])
+table = table.rename(columns = {'y_week' : 'week_name'})
 
 # Save results
 table.to_csv(DATA_PATH + 'variants_pivot.csv', index = False)
diff --git a/plots/results_genomics.py b/plots/results_genomics.py
@@ -35,7 +35,8 @@
 df_variants['date'] = pd.to_datetime(df_variants['date'])
 ## Results from multinomial analysis
 df_results = pd.read_csv(OUT_PATH + 'theta.csv')
-df_pivot =  pd.read_csv(DATA_PATH + 'variants_pivot.csv').rename(columns = {'t' : 'week', 'week' : 'week_name'})
+df_pivot =  pd.read_csv(DATA_PATH + 'variants_pivot.csv').rename(columns = {'t' : 'week'})
+
 df_results = df_results.merge(df_pivot[['week', 'week_name']], on = 'week')
 df_results['week_date'] = df_results.week_name.apply(lambda date: datetime.strptime(date + '-1', "%Y-%W-%w"))
 df_results = df_results.sort_values(by = 'week_date')