I need to customise the colour code for protein multiple sequence alignment (MSA), However the existing R packages only supports the predefined colour codes, which are single letter based. But, I have to assign my own colour scheme for a pair of letters (amino acid). I have gone through the packages like ggmsa
and ggplot2
etc., but failed to find the solution. I need to generate a figure as shown below,
I have followed the below script but could not serve my purpose,
library(tidyverse)
library(ggtree)
library(seqinr)
tree = read.tree("tree.newick")
msaplot(p=ggtree(tree), fasta = "msa.fasta")
msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "msa.fasta")
My fasta file is shown below,
msa.fasta
>Tl8
NI-NG-HD-NS-N*-NU
>T_X12
NI-NG-NI-NG-NI-NG-NI-NG
>T_T_x56
NI-NG-HD-NS-N*-NI-NG
My test tree file are shown below,
tree.newick
(tal8:0.49999997,t_temp5:0.47298786,t1:28.37858179);
Kindly help me to do the same.
Thanks in advance.