Dynamic Multiple Sequence Alignments in R and Shiny

msaR(msa, menu = TRUE, width = NULL, height = NULL, rowheight = 15,
  alignmentHeight = 225, overviewbox = TRUE, seqlogo = TRUE,
  colorscheme = "nucleotide", conservation = FALSE, markers = TRUE,
  metacell = FALSE, leftheader = TRUE, labels = TRUE, labelname = TRUE,
  labelid = TRUE, labelNameLength = 100, overviewboxWidth = "auto",
  overviewboxHeight = "fixed")

Arguments

msa

File or BioString Object representing a multiple Sequence Alignment.

menu

Optional. Default TRUE. Determines whether to include the interactive menu.

width

Optional. Default NULL. The width of the html widget element.

height

Optional. Default NULL. The height of the html widget element.

rowheight

Optional. Default 20. Height of a row in the MSA.

alignmentHeight

Optional. Default 225. Height of the MSA.

overviewbox

optional. Default TRUE. Include the overview box?

seqlogo

optional. Default TRUE. Include the seqlogo?

colorscheme

optional. Default "nucleotide". The color scheme to use. Can be one of the following: "buried","cinema","clustal","clustal2","helix","hydro","lesk","mae","nucleotide","purine","strand","taylor","turn","zappo"

conservation

optional. Default TRUE. Include the conservation widget?

markers

optional. Default TRUE. Include the alignment markers? These are the numbers along the top that

metacell

optional. Default FALSE. Include the per-sequence metadata.

leftheader

optional. Default TRUE. Include the header information.

labels

optional. Default TRUE. Include all of the sequence information msa Labels.

labelname

optional. Default TRUE. Include sequence name?

labelid

optional. Default TRUE. Include the labelid?

labelNameLength

optional. Default 100. Width of the Label Names.

overviewboxWidth

optional. Default. "auto". Can also be "fixed"

overviewboxHeight

optional. Default. "fixed". Can also be an integer value.

Examples

seqfile <- system.file("sequences","AHBA.aln",package="msaR") msaR(seqfile)
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in dirname(to): a character vector argument expected