Notebook size

[michalk8]

The notebook size (analysis_template.ipynb) is extremely large because of these plots:

• velocity_plot
• link_plot

[michalk8]

In the velocity plot, the GP now only uses 100 points (instead of allf points on the x-axis) to plot the error bounds, so that the size of the plot greatly reduced.
link_plotnow offers 2 subsampling strategies, with which user can control the #points (ideally < 1000). By default, sampling=None. The 2 strategies are:

• sampling='uniform': uniformly spaced points in the emedding (default step_size=30)
• sampling='density': sampling based on the density in the embedding (default sample_size=500)

Since we cannot really use precomputed distance matrix (especially in the case of distance='dpt'), this seems like the only option.