cohort_view update

barplot in "Total" column has vmin=0 and vmax=grand total.

cmapPy/visualization/cohort_view.py

@@ -10,22 +10,6 @@
 logger = logging.getLogger()
 
 
-def _add_row_percentages(s):
-    '''Convert all columns except for "Total" to a string
-    that shows the integer count as well as the percentage
-    of Total within the row.'''
-    s = s + 0
-    index = s.index
-    assert "Total" in index
-    total = s['Total']
-    for label, x in s.iteritems():
-        if label == "Total":
-            continue
-        s[label] = r'<span style="width:50%;float: left;text-align:right">{:,d} </span>\
-        <span style="font-size:1em;color:#888888;width:50%;text-align:left;float: right;padding-left:1em">({:.0%})</span>'.format(int(x), float(x) / total)
-    return s
-
-
 def cohort_view_table(df,
                       category_label="category_label",
                       category_order="category_order",
@@ -78,7 +62,8 @@ def cohort_view_table(df,
 
     # Test comopound fields
     cpd_fields = [c for c in df.columns if 'Test subset' in c]
-    df['Test Compounds Total'] = df[cpd_fields].sum(1)
+    if len(cpd_fields) != 0:
+        df['Test Compounds Total'] = df[cpd_fields].sum(1)
     df['Grand Total'] = df.iloc[:, :num_categories].sum(1)
     df = df.T
     df.index.name = None
@@ -97,8 +82,6 @@ def _fmt_total_percentages(x, total):
     <span style="font-size:1em;color:#FF7043;width:50%;text-align:left;float: right;padding-left:1em;font-weight:bold">
     ({:.0%})</span>'''.format(int(x), float(x) / total)
     return s
-
-    from IPython.display import display
 
 
 def _add_row_percentages(s):
@@ -117,45 +100,6 @@ def _add_row_percentages(s):
         ({:.0%})</span>'''.format(int(x), float(x) / total)
     return s
 
-# 
-# def cohort_view_table(df,
-#                       category_label="category_label",
-#                       category_order="category_order",
-#                       flags=[],
-#                       flag_display_labels=[],
-#                      add_percentages=True):
-# 
-#     
-#     df['Total'] = 1
-#     columns = ['Total'] + flags 
-#     df = (
-#         df
-#         .groupby([category_order, category_label])[columns]
-#         .sum()
-#         .sort_index(axis=0, level=category_order)
-#         .reset_index(level=[category_order])
-#         .drop(columns=category_order)
-#     )
-# 
-#     column_names = ["Total"] +  flag_display_labels 
-#     df.columns  = column_names
-#     df.index.names=['Category'] 
-# 
-#     df = df.T
-#     num_categories = len(df.columns)
-#     print "num_categories: {}".format(num_categories)
-# 
-#     # Test comopound fields
-#     cpd_columns = [c for c in df.columns if 'Test subset' in c]
-#     df['Test Compounds Total'] = df[cpd_columns].sum(1)
-#     df['Grand Total'] = df.iloc[:,:num_categories].sum(1)
-#     df = df.T
-#     df.index.name=None
-#     
-#     if add_percentages:
-#         df = df.transform(_add_row_percentages, axis=1)
-#     return df
-
 
 def display_cohort_stats_table(table, barplot_column):
     font_family = "Roboto"
@@ -164,9 +108,11 @@ def display_cohort_stats_table(table, barplot_column):
     # the last "total" sums
     group_ids = [x for x in table.index if 'Total' not in x]
 
+    barplot_max = table.loc[group_ids, barplot_column].sum()
+
     # Sum of numbers in Total column (excluding Grand Total, obviously)
     total = table.loc['Grand Total', 'Total']
-    return (
+    table_stylized = (
         table
         .style
         .format(
@@ -175,10 +121,9 @@ def display_cohort_stats_table(table, barplot_column):
         )
         .applymap(lambda x : 'text-align:center;')
         .applymap(lambda x: "border-left:solid thin #d65f5f", subset=idx[:, barplot_column])
-        .bar(subset=idx[group_ids, barplot_column], color='#FFDACF')
+        .bar(subset=idx[group_ids, barplot_column], color='#FFDACF', vmin=0, vmax=barplot_max)
         .applymap(lambda x: "padding:0.5em 1em 0.5em 1em")
         .applymap(lambda x: "background:#444;color:white;border:solid thin #000;font-weight:bold", subset=idx['Grand Total', :])
-        .applymap(lambda x: "border-top:solid thin #aaa", subset=idx['Test Compounds Total', :])
         .applymap(lambda x: "border-left:solid thin #ddd", subset=idx[:, 'Total'])
          .set_table_styles(
              [
@@ -223,4 +168,7 @@ def display_cohort_stats_table(table, barplot_column):
              ]
           )
         )
+    if 'Test Compounds Total' in table.index:
+        table_stylized = table_stylized.applymap(lambda x: "border-top:solid thin #aaa", subset=idx['Test Compounds Total', :])
 
+    return table_stylized

cmapPy/visualization/test_cohort_view.py

@@ -29,7 +29,7 @@ def testCohortView(self):
             flag_display_labels=column_names
 
             )
-        print table
+        print(table)
 #         plt.savefig("./test_files/cohort_view_test.html", dpi=150)