R语言实现多序列比对（MSA）可视化

BiocManager::install("treeio")
BiocManager::install("Biostrings")
BiocManager::install("ggtree")
install.packages("ggmsa")
install.packages("seqmagick")
install.packages("cowplot")

sequences <-system.file("extdata", "sample.fasta", package ="ggmsa")
ggmsa(sequences, 320, 360, color ="Clustal")

ggmsa(sequences, 320, 360, font = NULL,color = "Chemistry_AA")

library(Biostrings)
x <- readAAStringSet(sequences)
d <- as.dist(stringDist(x, method ="hamming")/width(x)[1])
library(ape)
tree <- bionj(d)
library(ggtree)
p <- ggtree(tree ) + geom_tiplab()
 
data = tidy_msa(x, 164, 213)
p + geom_facet(geom = geom_msa, data =data,  panel = 'msa', font = NULL, color= "Chemistry_AA") +xlim_tree(1)

f <- system.file("extdata","LeaderRepeat_All.fa", package = "ggmsa")
s <- readDNAStringSet(f)
strings <- as.character(s)
p1 <- ggmsa(s, font = NULL, color ='Chemistry_NT')
 
library(ggseqlogo)
library(cowplot)
 
p2 <- axis_canvas(p1, axis='x')+geom_logo(strings, 'probability')
pp <- insert_xaxis_grob(p1, p2,position="top", grid::unit(.05, "null"))
ggdraw(pp)