Using msaR

Zach Charlop-Powers

2021-09-22

Basic Usage

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)

Customized MSAs

msaR(seqfile, menu=F, overviewbox = F)

Protein MSA

# 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")

Use as a Shiny widget

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)
)