I would like to visualize tree with multiple sequence alignment.
din.newick file is shown below,
din.fasta alignment file shown below,
>org1 ATGCTA >org2 TAGCAT >org3 AGTAGT
I have tried the following code,
library(tidyverse) library(ggtree) library(seqinr) tree = read.tree("din.newick") msaplot(p=ggtree(tree), fasta = "din.fasta") msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "din.fasta")
The above mentioned code is generating tree with the alignment matrix, but the tree root tip labels are not visible. It is either overlapped with matrix or it is not at all visible. Kindly help me to fix this issue.