How to assign custom colour codes for Multiple sequence alignment (MSA)?
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@7ba17aca
Last seen 8 weeks ago
India

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, Expected output Sample image I tried with the following scripts but failed to complete my task for the test files as follows,

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
tree.newick
(tal8:0.49999997,t_temp5:0.47298786,t1:28.37858179);
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")

But with the above script I could only end up with single letter colour code without any changes. Therefore, Kindly help me to do the same.

Phylogenetics genomes R MultipleSequenceAlignment Bioconductor • 68 views
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