Update of figure plots and analysis

[constantinpape]

This builds on #43 by refactoring and updating plotting scripts as well as some analysis scripts.

Main changes:

• Refactor plotting scripts into one script per figure; add / extend scripts for plotting panels of figure 3 and 4; change figure 2C to display synapse counts in the same style as IHCs and SGNs; some cosmetic changes.
  • This includes functionality for plotting values over the run-length and octave bands.
• Update the ChReef analysis script so that the thresholds can be saved.

Remaining issues: I noticed two, likely related, issues in the ChReef transduction analysis:

• The thresholds that are determined are often NaN. (Easy to check by saving the thresholds to file)
• When applying the thresholds to the full cochlea, SGNs (in the main component) often still have the value 0 but all should have value 1 or 2. Maybe this happens when the nearest threshold is NaN?

Comment about plots for figure 4:

• Rather than having two separate figures for octave-based analysis of L/R it would be better to have them in the same plot and have two columns in the frequency band; see the current version of the figure: