Updating plots to be more powerful

[jgostick]

Fixes #3030

This PR changes a few of the behaviors of plot_coordinates and plot_connections:

• No longer uses plt.gca() to overwrite ax, it just uses the ax that is received.
• It now returns ax, which is crucial for the case of 3d plots since it deletes the received one (if 2D) and generates a new one.
• No longer scales color values between 0 and 1. It now plots colors it receives. Matplotlib will scale these automatically, but you can specify vmin and vmax.
• Some other changes are behind the scenes, like passing colors to array instead of colors in the LineCollection call.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.7%. Comparing base (cab63d0) to head (e109568).
⚠️ Report is 8 commits behind head on dev.

Additional details and impacted files

@@          Coverage Diff          @@
##             dev   #3031   +/-   ##
=====================================
  Coverage   87.7%   87.7%           
=====================================
  Files        151     151           
  Lines       8879    8879           
=====================================
  Hits        7792    7792           
  Misses      1087    1087           

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