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knitr::opts_chunk$set(echo = TRUE, message=FALSE)
msaR is a an htmlwidgets wrapper of the BioJS MSA viewer javascript library. msa will pass alignments to the BioJS MSA.
library(msaR) # read some sequences from a Multiple sequence alignment file. seqfile <- system.file("sequences","AHBA.aln", package="msaR") # display the MSA. msaR(seqfile, menu=F, overviewbox = F)
msaR(seqfile, menu=F, overviewbox = F)
# read some sequences from a Multiple sequence alignment file. proteinseqfile <- system.file("sequences","phosphoproteins.aln", package="msaR") # loading AA with ape. Can also use Biostrings proteins <- ape::read.FASTA(proteinseqfile, type="AA") # note the seqlogo will show up in your widget but # not the vignette static output msaR(proteins, menu=F, overviewbox = F, colorscheme = "clustal")
msaR can be used as a widget with the Shiny web application framework.
In ui.R
msaROutput("msa", width="100%")
In server.R
output$msa <- renderMsaR( msaR(seqfile) )
Any scripts or data that you put into this service are public.
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