I've been trying to run the example in the msa documentation. I get a fasta file, but no graph. Instead I get text detailing the msa file. I don't need to create a pdf, I just want to see the graph in Rstudio.
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)
myAlignment <- msa(mySeqs)
msaPrettyPrint(myAlignment, output="asis", askForOverwrite=FALSE)
\begin{texshade}{C:/Users/d.guillotin/AppData/Local/Temp/Rtmp6RWxwQ/seq2e0c4ae64ed7.fasta} \seqtype{P} \shadingmode{identical} \threshold{50} \showconsensus[ColdHot]{bottom} \shadingcolors{blues} \showsequencelogo[chemical]{top} \hidelogoscale \shownames{left} \nameseq{1}{PH4H Rattus norvegicus} \nameseq{2}{PH4H Mus musculus} \nameseq{3}{PH4H Homo sapiens} \nameseq{4}{PH4H Bos taurus} \nameseq{5}{PH4H Chromobacterium violaceum} \nameseq{6}{PH4H Ralstonia solanacearum} \nameseq{7}{PH4H Caulobacter crescentus} \nameseq{8}{PH4H Pseudomonas aeruginosa} \nameseq{9}{PH4H Rhizobium loti} \shownumbering{right} \showlegend \end{texshade}
