Alter IPython notebook.

Changes to many plots, added more interactivity to some plots.
Can now choose between plotting lineage ratios between 452 and 1600
genome datasets. Looks like 452 genomes are quite representative of
what's been sampled in the 1600 dataset in terms of lineage composition.

Added the option to plot particular segments in the stateTime plot (per
issue #14). Changes to LD plotting accompany the new LD calculator and
there's an extra freebie - circos-like plot for LD at the very end.
Starting to work on the option to plot everything in black and white.