[ENH] Silhouette plot: Accept distance matrix on input

[ales-erjavec]

Issue

Silhouette plot does not accept distance matrix on input.

Description of changes

• Accept either table or a distance matrix (with an attached table) on input. If distance matrix is provided the associated 'Distance' GUI controls are disabled.

Includes

• Code changes
• Tests
• Documentation

[codecov]

Codecov Report

Merging #4313 into master will increase coverage by <.01%.
The diff coverage is 95.27%.

@@            Coverage Diff             @@
##           master    #4313      +/-   ##
==========================================
+ Coverage   86.75%   86.75%   +<.01%     
==========================================
  Files         396      396              
  Lines       71660    71738      +78     
==========================================
+ Hits        62169    62238      +69     
- Misses       9491     9500       +9

[ajdapretnar]

The widget crashes on Bhattacharyya distance. The rest works fine.

---------------------------- ValueError Exception -----------------------------
Traceback (most recent call last):
  File "/Users/ajda/orange/orange-canvas-core/orangecanvas/scheme/signalmanager.py", line 936, in __process_next
    if self.__process_next_helper(use_max_active=True):
  File "/Users/ajda/orange/orange-canvas-core/orangecanvas/scheme/signalmanager.py", line 974, in __process_next_helper
    self.process_node(selected_node)
  File "/Users/ajda/orange/orange-canvas-core/orangecanvas/scheme/signalmanager.py", line 605, in process_node
    self.send_to_node(node, signals_in)
  File "/Users/ajda/orange/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 792, in send_to_node
    self.process_signals_for_widget(node, widget, signals)
  File "/Users/ajda/orange/orange-widget-base/orangewidget/workflow/widgetsscheme.py", line 833, in process_signals_for_widget
    widget.handleNewSignals()
  File "/Users/ajda/orange/orange3/Orange/widgets/visualize/owsilhouetteplot.py", line 247, in handleNewSignals
    self._update()
  File "/Users/ajda/orange/orange3/Orange/widgets/visualize/owsilhouetteplot.py", line 375, in _update
    self._matrix[~mask, :][:, ~mask], labels, metric="precomputed")
  File "/Users/ajda/miniconda3/envs/o3/lib/python3.7/site-packages/sklearn/metrics/cluster/_unsupervised.py", line 234, in silhouette_samples
    **kwds))
  File "/Users/ajda/miniconda3/envs/o3/lib/python3.7/site-packages/sklearn/metrics/pairwise.py", line 1592, in pairwise_distances_chunked
    n_jobs=n_jobs, **kwds)
  File "/Users/ajda/miniconda3/envs/o3/lib/python3.7/site-packages/sklearn/metrics/pairwise.py", line 1718, in pairwise_distances
    check_non_negative(X, whom=whom)
  File "/Users/ajda/miniconda3/envs/o3/lib/python3.7/site-packages/sklearn/utils/validation.py", line 979, in check_non_negative
    raise ValueError("Negative values in data passed to %s" % whom)
ValueError: Negative values in data passed to `pairwise_distances`. Precomputed distance  need to have non-negative values.
-------------------------------------------------------------------------------

[ales-erjavec]

Distances should be non-negative and that includes Bhattacharyya distance which by definition cannot be negative (probably a floating point math rounding issue in the implementation).

[janezd]

If Bhattacharyya distance can return negative distances, it has to be fixed. Silhouette won't be the only widget affected. @AndrejaKovacic, could you check please?