inst/examples/plot-msa.R

In rphast: Interface to 'PHAST' Software for Comparative Genomics

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
unzip(exampleArchive, "ENr334-100k.maf")
m <- read.msa("ENr334-100k.maf")
plot.msa(m)
plot.msa(m[, 1:2])
plot.msa(m[,1:20])
plot.msa(m[1:3,1:40])
plot.msa(m[,1:100])
plot.msa(m[,1:50], refseq=NULL)
plot.msa(m[,1:50], refseq=NULL, nuc.text=rep(paste(rep("ASDFG", 10), sep="", collapse=""), 2),
         nuc.text.col=c("black", "red"), nuc.text.pos=c("top"))
rm(m)
unlink("ENr334-100k.maf")