Custom colours for disagreements to consensus using ggmsa()

[Luke Baton]

Hi,

Is it possible to specify custom colours when plotting disagreements to the consenus of a multiple sequence alignment when using the "consensus_views" argument of the ggmsa() function?

I have been able to create custom colours when NOT using the "consensus_views" argument (as described here: https://yulab-smu.top/ggmsa/articles/guides/Color_schemes_And_Font_Families.html).

However, I'd like to plot a multiple sequence alignment using either only two colours (say, grey and black), or 5 colours (grey, red, blue, green and yellow), where conserved sites are grey and polymorphic sites are either all black (or different colours for each of the 4 nucleotides).

Any help would be greatly appreciated.

Luke