Fixed ppm handling and added figure saving

[fabian178]

Description

I added figure saving in the plotting functions and fixed a pseudocount error in the ppm_to_pwm conversion function. The problem occurs when a ppm with a 0 entry is converted to a pwm, there is no check for 0 entries, and the resulting pwm has a -inf entry, due to log2(0). This is fixed by adding a small pseudo count to the ppm and then normalising it such that all rows add to 1. This slightly changes the ppm, so imo, it is best to put this pseudo count check into the function that reads in the ppm.

Fixes #.

Checklist:

• [x ] I have performed a self-review of my own code.
• [x ] I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.