Plot improvements feb 26

[vegardkv]

• Intersecting contours
• Remove redundant/unused code
  • Commented code
  • Print statements
  • Dump to file
• Numeric formatting of colorbars and axes (use e.g. "tickformat = '.1f'")
• Reduce the number of plots to 3: silhouette, biplot and the final feature plot
• Add boundaries to U-matrix in final feature plot
• Use vertical color bars on feature plots
• Update and add dendrogram plot (different script)
• Clean up code
• Clean up dependencies (pyproject.toml)

NB! Found a bug where weights are (unintentionally) modified after the first feature plot. This seems to have implications for contour lines, including the equilibrium line. Need to dive a bit deeper into what happens. The latest commit per 18. feb implements a fix with a ".copy()" invocation, but we might want to revert this. The expected changes we need (but this needs verification):

• All current contour lines are calculated on the "doubly normalized" data (I believe). I don't think this is critical. We can adjust the contour levels and achieve a very similar plot, since the second normalization is just a linear transformation.
• Equilibrium lines will be moved. These are set based on specific thresholds and are expected to refer to values on the normalized data, and not on the doubly normalized data. Need to take extra care when handling this, so that we are sure this gets right.
• PC lines seems only marginally affected.

[vegardkv]

Above was not a bug, but some less intuitive handling of variables. This is now fixed.

Additional tasks:

• Create large variant of cluster plot where samples are printed vertically within each node. The current cluster plot can change to have number of nodes show instead