Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE)
## -----------------------------------------------------------------------------
library(msaR)
# read some sequences from a Multiple sequence alignment file.
seqfile <- system.file("sequences","AHBA.aln", package="msaR")
# display the MSA.
msaR(seqfile, menu=F, overviewbox = F)
## -----------------------------------------------------------------------------
msaR(seqfile, menu=F, overviewbox = F)
## -----------------------------------------------------------------------------
# read some sequences from a Multiple sequence alignment file.
proteinseqfile <- system.file("sequences","phosphoproteins.aln", package="msaR")
# loading AA with ape. Can also use Biostrings
proteins <- ape::read.FASTA(proteinseqfile, type="AA")
# note the seqlogo will show up in your widget but
# not the vignette static output
msaR(proteins, menu=F, overviewbox = F, colorscheme = "clustal")
## ---- eval=FALSE--------------------------------------------------------------
# msaROutput("msa", width="100%")
## ---- eval=FALSE--------------------------------------------------------------
# output$msa <- renderMsaR(
# msaR(seqfile)
# )
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