Help for package msaR

Title:

Multiple Sequence Alignment for R Shiny

Version:

0.6.0

Description:

Visualizes multiple sequence alignments dynamically within the Shiny web application framework.

Depends:

R (≥ 3.2.2)

License:

BSL-1.0

Imports:

ape, htmlwidgets

Suggests:

Biostrings, knitr, rmarkdown, testthat (≥ 3.0.0)

RoxygenNote:

7.1.2

VignetteBuilder:

knitr

Config/testthat/edition:

NeedsCompilation:

Packaged:

2021-09-22 02:54:25 UTC; zachcp

Author:

Benedikt Rauscher [aut, cph], Zachary Charlop-Powers [cre, aut]

Maintainer:

Zachary Charlop-Powers <zach.charlop.powers@gmail.com>

Repository:

CRAN

Date/Publication:

2021-09-22 04:30:09 UTC

check_lengths

Description

check_lengths

Usage

.check_lengths(seqlist)

Arguments

seqlist

optimistic loading can lead to issues. All MSAs should have identical length. if not theres a problem.

as.fasta

Description

functionality to convert objects to a fasta string. Currently this can handle character objects which are interpreted as filenames or several of the popular means of storing sequence data: DNAbin, DNAStringSet, AAStringSet, RNAStringSet, BStringSet, DNAMultipleAlignment, RNAMultipleAlignment, or AAMultipleAlignment.

Usage

as.fasta(seqs)

Arguments

seqs

(Required.) the sequence/alignment to be displayed. A character vector, DNAbin, DNAStringSet, AAStringSet, or RNAStringSet.

Value

A character string in fasta format.

Examples

seqfile <- system.file("sequences","AHBA.aln",package="msaR")
as.fasta(seqfile)
help("as.fasta")

## Not run: 
if (requireNamespace("Biostrings")) {
   seqs <- readDNAStringSet(seqfile)
   as.fasta(seqs)
 }

## End(Not run)

as.sequences

Description

functionality to convert sequence objects into R lists that can be serialized to JS as JSON. Currently, this can handle character objects which are interpreted as filenames or several of the popular means of storing sequence data: DNAbin, DNAStringSet, AAStringSet, RNAStringSet, BStringSet, DNAMultipleAlignment, RNAMultipleAlignment, or AAMultipleAlignment.

Usage

as.sequences(seqs)

Arguments

seqs

(Required.) the sequence/alignment to be displayed. A character vector, DNAbin, DNAStringSet, AAStringSet, or RNAStringSet.

Value

A list of named lists where each sublist has name, id, and seq members.

Examples

seqfile <- system.file("sequences","AHBA.aln",package="msaR")
as.sequences(seqfile)
help("as.sequences")

## Not run: 
if (requireNamespace("Biostrings")) {
   seqs <- readDNAStringSet(seqfile)
   as.sequences(seqs)
 }

## End(Not run)

msaR

Description

Dynamic Multiple Sequence Alignments in R and Shiny

Usage

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 = FALSE,
  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 FALSE. 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)

Widget output function for use in Shiny

Description

Widget output function for use in Shiny

Usage

msaROutput(outputId, width = "100%", height = "100%")

Arguments

outputId

output id

width

width

height

height

Widget render function for use in Shiny

Description

Widget render function for use in Shiny

Usage

renderMsaR(expr, env = parent.frame(), quoted = FALSE)

Arguments

expr

expr

env

env

quoted

quoted