category label

cmapPy/visualization/stratogram.py

@@ -21,7 +21,8 @@
 
 def stratogram(
  data,
- category,
+ category_definition,
+ category_label,
  category_order,
  metrics,
  column_display_names,
@@ -39,15 +40,17 @@ def stratogram(
  '''
  Create a stratogram of the data. A stratogram is a grid of histograms
  of various metrics computed for a set of data points, stratified by a
- "category" variable. Each column of the grid is one metric, and each row
+ "category_definition" variable. Each column of the grid is one metric, and each row
  depicts a stratum of the data.
  @param data: Pandas DataFrame where each row is a data point and the
  metrics and other variables are in the columns.
- @param category: string name of the column that defines the stratum/
+ @param category_definition: string name of the column that defines the stratum/
  category of each data point.
+ @param category_label: string name of the column that defines the stratum/
+ label for each data point.
  @param category_order: string name of the integer column that defines
  the order in which each stratum should be plotted in the rows. There
- should be a one-to-one map between the category and category_order
+ should be a one-to-one map between the category_definition and category_order
  variables. 
  @param metrics: list of column names containing numberical values
  whose histogram is plotted.
@@ -68,14 +71,14 @@ def stratogram(
  column_display_names = [name + "\n" for name in column_display_names]
 
  # Make sure necessary columns are in the dataframe
- assert category in df.columns
+ assert category_definition in df.columns
  assert category_order in df.columns
 
  logger.info('Validating the table')
  for metric in metrics:
  assert metric in df.columns, metric
 
- # Update category order to "remove" non-existent categories
+ # Update category_definition order to "remove" non-existent categories
  dict_new_order = {x:i for i, x in enumerate(sorted(df[category_order].unique().tolist()))}
  df[category_order] = df[category_order].apply(lambda x:dict_new_order[x])
  n_rows = df[category_order].nunique()
@@ -86,14 +89,19 @@ def stratogram(
  gs.update(wspace=0.0, hspace=0.0)
 
  # Count the total number of test compounds
- test_categories = [c for c in df[category].dropna().unique() if is_test_category(c)]
- num_test_compounds = len(df[df[category].isin(test_categories)])
+ test_categories = [c for c in df[category_definition].dropna().unique() if is_test_category(c)]
+ num_test_compounds = len(df[df[category_definition].isin(test_categories)])
 
- # Group the data by the category variable and for each stratum
+ # Group the data by the category_definition variable and for each stratum
  # Plot a row of histograms in the grid.
- grouped = df.groupby(category)
+ grouped = df.groupby(category_definition)
  for name, group in grouped:
  row_is_test_compounds = is_test_category(name)
+ name = group[category_label].unique()
+ print name
+ assert len(name) == 1
+ name = name[0]
+
  group.name = name
  row_label = name
  n_points = len(group)

cmapPy/visualization/test_stratogram.py

@@ -20,7 +20,8 @@ def testStratogram(self):
  column_names = ['Strength', 'Reproducibility', 'specificity', 'magnitude']
  stratogram.stratogram(
  df,
- category="category_label",
+ category_definition="category_label",
+ category_label="category_label_abridged",
  category_order="category_order",
  metrics=metrics,
  figsize=(20,15),
@@ -32,7 +33,6 @@ def testStratogram(self):
  ylabel_fontcolor="#555555",
  fontfamily="Roboto"
  )
-# plt.show()
  plt.savefig("./test_files/stratogram_test.png", dpi=150)