updates evaluate_classifications

rescript/cross_validate.py

@@ -166,7 +166,7 @@ def evaluate_classifications(ctx,
  expected_taxonomies,
  observed_taxonomies,
  labels=None):
- volatility = ctx.get_action('longitudinal', 'volatility')
+ lineplot = ctx.get_action('vizard', 'lineplot')
  # Validate inputs.
  if len(expected_taxonomies) != len(observed_taxonomies):
  raise ValueError('Expected and Observed Taxonomies do not match. '
@@ -201,10 +201,11 @@ def evaluate_classifications(ctx,
  # convert index to strings
  precision_recall.index = pd.Index(
  [str(i) for i in range(1, len(precision_recall.index) + 1)], name='id')
- plots, = volatility(metadata=q2.Metadata(precision_recall),
- state_column='Level',
- default_group_column='Dataset',
- default_metric='F-Measure')
+ plots, = lineplot(metadata=q2.Metadata(precision_recall),
+ x_measure='Level',
+ y_measure='F-Measure',
+ group_by='Dataset',
+ title='RESCRIPt Evaluate Classifications')
  return plots
 
 

rescript/plugin_setup.py

@@ -82,7 +82,7 @@
  'CC BY-SA 4.0. To learn more, please visit https://unite.ut.ee/cite.php '
  'and https://creativecommons.org/licenses/by-sa/4.0/.')
 
-VOLATILITY_PLOT_XAXIS_INTERPRETATION = (
+LINEPLOT_XAXIS_INTERPRETATION = (
  'The x-axis in these plots represents the taxonomic '
  'levels present in the input taxonomies so are labeled numerically '
  'instead of by rank, but typically for 7-level taxonomies these will '
@@ -225,7 +225,7 @@
  'sets of true taxonomic labels to the predicted taxonomies for the '
  'same set(s) of features. Output an interactive line plot of '
  'classification accuracy for each pair of expected/observed '
- 'taxonomies. ' + VOLATILITY_PLOT_XAXIS_INTERPRETATION),
+ 'taxonomies. ' + LINEPLOT_XAXIS_INTERPRETATION),
  citations=[citations['bokulich2018optimizing'],
  citations['bokulich2017q2']]
 )
@@ -395,7 +395,7 @@
  'unique labels, taxonomic entropy, and the number of features that '
  'are (un)classified at each taxonomic level. This action is useful '
  'for both reference taxonomies and classification results. ' +
- VOLATILITY_PLOT_XAXIS_INTERPRETATION),
+ LINEPLOT_XAXIS_INTERPRETATION),
  citations=[citations['bokulich2017q2']]
 )