[FIX] t-SNE speed-ups

[pavlin-policar]

Issue

t-SNE was slow

Description of changes

• The multiscale option makes things slow for larger data sets, so turn it off by default.
• Use faster approximation setting for Barnes-Hut
• Update t-SNE plot only at the start and at the end, avoiding potentially many redraws
• Selecting data in t-SNE was slow because transform was being called. Avoid this.

Includes

• Code changes
• Tests
• Documentation

[lanzagar]

This can probably be removed now. In any case the comment is no longer true.

[pavlin-policar]

This cannot be removed because, at the start of the optimization, we have to draw something, so we just draw some random points, because the graph widget needs some data to be shown. However, we'd like to replace this random data with something slightly more meaningful as soon as possible, so setting this to True here will ensure that after the first batch of iterations is done, the widget will display something better than random data.

[codecov]

Codecov Report

Merging #3592 into master will increase coverage by <.01%.
The diff coverage is 93.33%.

@@            Coverage Diff             @@
##           master    #3592      +/-   ##
==========================================
+ Coverage   83.98%   83.98%   +<.01%     
==========================================
  Files         370      370              
  Lines       66976    66984       +8     
==========================================
+ Hits        56249    56256       +7     
- Misses      10727    10728       +1