Nothing
read.fasta <- function
### Read sequences in FASTA format into a named character vector
(infile
### Name of the sequence file
){
infile
}
##debug(read.fasta)
### Letters in the DNA alphabet, used to auto-detect sequence type
dna.letters <- c("*","A","T","G","C")
### DNA identity substitution matrix.
dna.identity <- matrix(0,nrow=length(dna.letters),ncol=length(dna.letters),
dimnames=list(dna.letters,dna.letters))
diag(dna.identity) <- 1
dna.identity['*','*'] <- 0
seqs.to.mat <- function
### Calculate pairwise differences between sequences using a
### substitution matrix.
(seq.vec,
### DNA or protein sequences.
subs.mat=NULL){
### Substitution matrix with dimnames that match the letters used in
### the sequence data, or a character vector that specifies a common
### substitution matrix (as defined in the Biostrings package). NULL
### specifies that we will guess a suitable substitution matrix to
### match your input sequences (DNA=>identity, protein=>BLOSUM62).
if(is.null(names(seq.vec)))names(seq.vec) <- seq.vec
chars <- sapply(seq.vec,nchar)
seqsum <- table(chars)
chars
### The matrix of distances between each input sequence, with dimnames
### corresponding to either the sequences, or the sequence names (if
### they exist)
}
##debug(seqs.to.mat)
make.logo.ps <- function
### Create a logo using weblogo, then read it in using grImport
(helices,
### Sequences to plot in the logo
psbase
### Base filename for the logo postscript and xml files, should be the
### full path name except for the trailing .ps
){
psfile <- paste(psbase,'ps',sep='.')
helices
### Grid picture grob as read using readPicture
}
##debug(make.logo.ps)
sublogo.dendrogram <- function
### Main function for drawing sublogo dendrograms.
(M,
### difference matrix as constructed by seqs.to.mat (although in
### principle any object with a valid as.dist method could be used)
main='',
### plot title
subtit=NULL,
### plot subtitle
base=tempfile(),
### base file name for temporary logo files
cutline=150,
### Distance for cutting the tree. Draw a sublogo for each
### leaf. Normally you will plot once, then inspect the dendrogram to
### determine which is a good value for cutline, then plot again using
### your chosen cutline.
dend.width=30,
### Percent of the plot to be occupied by the dendrogram. The logos
### will be displayed with equal widths on either side.
cex=1
### character expansion factor for the dendrogram
){
hc <- hclust(as.dist(M),method="average")
hc
### The dendrogram from the call to hclust
}
##debug(sublogo.dendrogram)
sublogo <- function
### Draw a sublogo dendrogram for a sequence motif.
(seqs,
### Character vector of DNA or protein sequences (optionally named
### with sequence labels).
mat=NULL,
### Substitution matrix passed to seqs.to.mat.
...
### Other arguments to pass to sublogo.dendrogram (see that help page
### for a full description).
){
sublogo.dendrogram(seqs.to.mat(seqs,mat),...)
}
.result <- list(
dna.identity = list(
description = "DNA identity substitution matrix.", format = "",
title = "dna identity"),
dna.letters = list(
description = "Letters in the DNA alphabet, used to auto-detect sequence type",
format = "", title = "dna letters"),
make.logo.ps = list(
description = "Create a logo using weblogo, then read it in using grImport",
`item{helices}` = "Sequences to plot in the logo", `item{psbase}` = "Base filename for the logo postscript and xml files, should be the\nfull path name except for the trailing .ps",
value = "Grid picture grob as read using readPicture", format = "",
title = "make logo ps"),
read.fasta = list(
description = "Read sequences in FASTA format into a named character vector",
`item{infile}` = "Name of the sequence file", format = "",
title = "read fasta"),
seqs.to.mat = list(
description = "Calculate pairwise differences between sequences using a\nsubstitution matrix.",
`item{seq.vec}` = "DNA or protein sequences.", `item{subs.mat}` = "Substitution matrix with dimnames that match the letters used in\nthe sequence data, or a character vector that specifies a common\nsubstitution matrix (as defined in the Biostrings package). NULL\nspecifies that we will guess a suitable substitution matrix to\nmatch your input sequences (DNA=>identity, protein=>BLOSUM62).",
value = "The matrix of distances between each input sequence, with dimnames\ncorresponding to either the sequences, or the sequence names (if\nthey exist)",
format = "", title = "seqs to mat"),
sublogo = list(
description = "Draw a sublogo dendrogram for a sequence motif.",
`item{seqs}` = "Character vector of DNA or protein sequences (optionally named\nwith sequence labels).",
`item{mat}` = "Substitution matrix passed to \\code{\\link{seqs.to.mat}}.",
`item{\\dots}` = "Other arguments to pass to \\code{\\link{sublogo.dendrogram}} (see that help page\nfor a full description).",
format = "", title = "sublogo"),
sublogo.dendrogram = list(
description = "Main function for drawing \\code{\\link{sublogo}} dendrograms.",
`item{M}` = "difference matrix as constructed by \\code{\\link{seqs.to.mat}} (although in\nprinciple any object with a valid as.dist method could be used)",
`item{main}` = "plot title", `item{subtit}` = "plot subtitle",
`item{base}` = "\\code{base} file name for temporary logo files",
`item{cutline}` = "Distance for cutting the tree. Draw a \\code{\\link{sublogo}} for each\nleaf. Normally you will plot once, then inspect the dendrogram to\ndetermine which is a good value for \\code{cutline}, then plot again using\nyour chosen \\code{cutline}.",
`item{dend.width}` = "Percent of the plot to be occupied by the dendrogram. The logos\nwill be displayed with equal widths on either side.",
`item{cex}` = "character expansion factor for the dendrogram",
value = "The dendrogram from the call to hclust", format = "",
title = "sublogo dendrogram"))
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