Supports linking ggtreeExtra

[xiangpin]

update geom_msa and msa_data to support linking ggtreeExtra.

library(ggmsa)
library(ggplot2)
library(ggtree)
library(ggtreeExtra)
library(Biostrings)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")

x <- readAAStringSet(protein_sequences)
d <- as.dist(stringDist(x, method = "hamming")/width(x)[1])
library(ape)
tree <- bionj(d)

data = tidy_msa(x, 164, 213)
p1 <- ggtree(tree) + geom_tiplab(size=2)

p2 <- p1 +
      geom_fruit(
          data = data,
          geom = geom_msa,
          offset = 1,
          pwidth =5
      )
p2

[xiangpin]

linking geom_facet of ggtree.

library(ggmsa)
library(ggplot2)
protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
library(Biostrings)
x <- readAAStringSet(protein_sequences)
d <- as.dist(stringDist(x, method = "hamming")/width(x)[1])
library(ape)
tree <- bionj(d)
library(ggtree)
p <- ggtree(tree) + geom_tiplab(size=2)

data = tidy_msa(x, 164, 213)
p <- p +
     geom_facet(
         geom = geom_msa,
         data = data,
         panel = 'msa',
         #font = NULL,
         color = "Chemistry_AA") +
     xlim_tree(1.5)

p <- facet_widths(p, width=c(1, 2))
p