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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)
)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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