Add default charge up to precursor charge in plotSpectraPTM

[guideflandre]

Following a discussion with @lgatto, we thought it would be interesting to include a charge parameter in plotSpectraPTM.

By default, the charge used to be set to 1, which missed quite a few fragments when the charge state of the precursor ion is higher than 2. Thus instead of having to manually include the charge state, a simple (big !) improvement is to set the default charge state a spectrum instance to be 1:precursorCharge(x).

It does make a huge difference and it integrates well with the variable modifications by allowing a list (or not) of charge values passed to labelFragments(). I believe this is the most straight-forward way to include the charge state in the spectra.

I bumped the version to 1.17.1 since there has been a devel update and I updated the NEWS

[guideflandre]

I have made a couple changes:

1. Both plotSpectraPTM and labelFragments now have a z and allCharges parameter.
2. The user can input a custom numeric vector with charge states for every spectrum provided. By default, z = NULL and allCharges = TRUE. With allCharges = TRUE, the fragments are calculated with charge states of 1 to the given charge OR, if z = NULL, to the precursor charge. If allCharges = FALSE, only the provided charge state is calculated.
3. The user cannot provide a custom charge while simultaneously asking for variable modifications in plotSpectraPTM as its length would not be the same.

Either way, the default options are most likely going to be used: all fragments with charge states 1:precursorCharge(x).

[guideflandre]

And I added the PSMatch logo to thje README for better visibility