ggmsa | Visualizing publication-quality multiple sequence alignment | Genomics library

I have many amino acids sequences like in a fasta format that I did multiple sequence alignment. I was trying to plot something like binary code as heatmap. If it had a change it would be red, if it did not change would be yellow, for example.

I came across to msaplot from ggtreepackage. I also checked ggmsa package for that. But so far, I did not get what I wanted. So basically I wanted to:

1. change the multiple sequence alignment to a binary matrix (if the amino differs from the reference sequence, plot x, if not y)

2. plot as a heatmap

A multiple sequence alignment is something like this for those who don't know.

I know that I should provide some type of data example but I am not sure how to create an example of multiple sequence alignment

if you install ggmsa you can have an example of the data and plot in r using: