R/saveAlignments.R
In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer
Defines functions
saveAlignments
write.phylip_html
splitStrByBlock
checkMotifCons
Documented in
saveAlignments
checkMotifCons <- function(motifConsensus){
if(length(motifConsensus)){
stopifnot("motifConsensus must be an object of DNAStringSet"=
is(motifConsensus, "DNAStringSet"))
af <- alphabetFrequency(motifConsensus)
af <- colSums(af)
stopifnot("motifConsensus can only contain 'A', 'C', 'G', 'T', 'N'"=
sum(lengths(motifConsensus))==
sum(af[c("A", "C", "G", "T", "N")]))
}
}
splitStrByBlock <- function(s, block, FUN, FUN.VALUE=character(1L), ...){
s <- split(s, rep(seq.int(ceiling(length(s)/block)),
each=block)[seq_along(s)])
vapply(s, FUN=FUN, FUN.VALUE = FUN.VALUE, ...)
}
write.phylip_html <- function(x, filepath, block=80){
x <- as.character(x)
x100 <- strsplit(x, split="")
n <- length(x100[[1]])
N <- ceiling(n/block)
x100 <- lapply(x100, function(.ele) {
splitStrByBlock(.ele, block=block, FUN=paste, collapse="")
})
blank <- c("<br/>", "<br/>")
x100 <- do.call(rbind, x100)
x100 <- apply(x100, 2, FUN=function(.ele){
paste("<p>", c(.ele, blank), "</p>")
})
x100_n <- paste("<p>", c(names(x), blank), "</p>")
x100_n <- rep(c("<div>", x100_n, "</div>"), N)
counter <- lapply(unique(c(seq.int(N-1)*block, n)), function(.ele){
paste("<p>",
c(.ele, rep("<br/>", length(x)-1), blank),
"</p>")
})
counter <- unlist(counter)
html <- c("<!DOCTYPE html><html><head><title>",
basename(filepath),
"</title>",
"<style>",
"#align { margin-left: 5px; width: 100%; font-family: monospace;}",
"#seqnames,#sequences,#counts { float: left}",
"#seqnames { max-width: 20%; }",
"#sequences {width: auto; min-width: 700px; margin-left: 20px;}",
"#counts { width: auto; align: 'left'}",
".space { margin-right: 12px;}",
"p {margin: 0px;}",
"</style>",
'<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.0/jquery.min.js"></script>',
"<script>",
'$(document).ready(function(){',
"var currentMousePos = { x: -1, y: -1};",
'$("#sequences").html(function(i,el) {',
"return el.replace(/((A|C|G|T|N|-){10})/g, '$1<span class=\"space\"></span>')",
".replace(/A/g, '<span style=\"color:green\">A</span>')",
".replace(/C/g, '<span style=\"color:orange\">C</span>')",
".replace(/G/g, '<span style=\"color:red\">G</span>')",
".replace(/T/g, '<span style=\"color:blue\">T</span>')",
".replace(/U/g, '<span style=\"color:blue\">U</span>');",
'});',
"});",
"</script>",
"</head><body>",
"<h1>Enhancer homologs multiple alignments</h1>",
"<div id='align'>",
"<div id='seqnames'>", x100_n, "</div>",
"<div id='sequences'>", x100, "</div>",
"<div id='counts'>", counter, "</div>",
"</div></body></html>")
writeLines(html, filepath)
}
#' @importFrom Biostrings consensusMatrix DNAStringSet write.phylip
#' matchPattern alphabetFrequency injectHardMask
#' @importFrom IRanges IRangesList Views
#' @importFrom utils write.csv
saveAln <- function (x, filepath, motifConsensus, format) {
stopifnot("input must be an object of MultipleAlignment"=
inherits(x, "MultipleAlignment"))
checkMotifCons(motifConsensus)
## get consensus
enhancer <- strsplit(as.character(x@unmasked[1]), "")[[1]]
cons <- consensusMatrix(x, baseOnly=TRUE)
consid <- apply(cons[rownames(cons) %in% c("A", "C", "G", "T"), ,
drop=FALSE], 2, which.max)
consid[apply(cons[rownames(cons) %in% c("A", "C", "G", "T"), ,
drop=FALSE], 2, max)<2] <-
which(!rownames(cons) %in% c("A", "C", "G", "T"))[1]
cons <- rownames(cons)[consid]
cons[cons!=enhancer] <- "-"
cons <- paste(cons, collapse = "")
cons_m <- gsub("-", "N", cons)
cons <- DNAStringSet(cons)
names(cons) <- "Consensus"
x@unmasked <- c(x@unmasked, cons)
## search binding sites
if(length(motifConsensus)){
mt <- lapply(motifConsensus, function(.ele)
matchPattern(pattern = .ele, subject = cons_m))
mt <- mt[lengths(mt)>0]
mt <- unlist(IRangesList(mt))
involved_motifs <- sort(mt)
mt <- reduce(mt)
if(length(mt)){
m <- Views(cons_m, start = start(mt), end = end(mt))
m <- injectHardMask(m, letter="-")
m <- DNAStringSet(m)
names(m) <- "motifConsensus"
x@unmasked <- c(x@unmasked, m)
write.csv(involved_motifs, file = paste0(sub(paste0(".",format,"$"),
"", filepath),
".motifConsensus.info.csv"),
row.names=FALSE)
}
}
if(format=="txt"){
write.phylip(x, filepath = filepath)
}else{
write.phylip_html(x, filepath = filepath)
}
}
#' output alignments
#' @description Save enhancer homologs to file in phylip format.
#' @param al output of \link{alignment}.
#' @param output_folder output folder.
#' @param motifConsensus Transcription factor binding consensus.
#' @param format The format of output files.
#' Available formats are 'txt' and 'html'. Default is 'txt'.
#' @export
#' @return The I/O status.
#' @examples
#' al <- readRDS(system.file("extdata", "al.rds",
#' package="enhancerHomologSearch"))
#' tmpfolder <- tempdir()
#' library(MotifDb)
#' motifs <- query(MotifDb, "JASPAR_CORE")
#' consensus <- sapply(motifs, consensusString)
#' consensus <- DNAStringSet(gsub("\\?", "N", consensus))
#' saveAlignments(al, output_folder=tmpfolder, motifConsensus=consensus)
saveAlignments <- function(al,
output_folder=tempdir(),
motifConsensus=NULL,
format=c("txt", "html")){
checkMotifCons(motifConsensus)
format <- match.arg(format)
if(!file.exists(output_folder)){
dir.create(output_folder)
}
if(length(names(al))!=length(al)){
names(al) <- paste0("aln", seq_along(al), ".phylip.", format)
}else{
names(al) <- paste0(names(al), ".phylip.", format)
}
null <- mapply(saveAln, x=al,
filepath = file.path(output_folder, names(al)),
MoreArgs=list(motifConsensus = motifConsensus,
format=format))
return(invisible(null))
}
jianhong/enhancerHomologSearch documentation built on May 7, 2024, 11:43 a.m.
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Defines functions saveAlignments write.phylip_html splitStrByBlock checkMotifCons
Documented in saveAlignments
checkMotifCons <- function(motifConsensus){
if(length(motifConsensus)){
stopifnot("motifConsensus must be an object of DNAStringSet"=
is(motifConsensus, "DNAStringSet"))
af <- alphabetFrequency(motifConsensus)
af <- colSums(af)
stopifnot("motifConsensus can only contain 'A', 'C', 'G', 'T', 'N'"=
sum(lengths(motifConsensus))==
sum(af[c("A", "C", "G", "T", "N")]))
}
}
splitStrByBlock <- function(s, block, FUN, FUN.VALUE=character(1L), ...){
s <- split(s, rep(seq.int(ceiling(length(s)/block)),
each=block)[seq_along(s)])
vapply(s, FUN=FUN, FUN.VALUE = FUN.VALUE, ...)
}
write.phylip_html <- function(x, filepath, block=80){
x <- as.character(x)
x100 <- strsplit(x, split="")
n <- length(x100[[1]])
N <- ceiling(n/block)
x100 <- lapply(x100, function(.ele) {
splitStrByBlock(.ele, block=block, FUN=paste, collapse="")
})
blank <- c("<br/>", "<br/>")
x100 <- do.call(rbind, x100)
x100 <- apply(x100, 2, FUN=function(.ele){
paste("<p>", c(.ele, blank), "</p>")
})
x100_n <- paste("<p>", c(names(x), blank), "</p>")
x100_n <- rep(c("<div>", x100_n, "</div>"), N)
counter <- lapply(unique(c(seq.int(N-1)*block, n)), function(.ele){
paste("<p>",
c(.ele, rep("<br/>", length(x)-1), blank),
"</p>")
})
counter <- unlist(counter)
html <- c("<!DOCTYPE html><html><head><title>",
basename(filepath),
"</title>",
"<style>",
"#align { margin-left: 5px; width: 100%; font-family: monospace;}",
"#seqnames,#sequences,#counts { float: left}",
"#seqnames { max-width: 20%; }",
"#sequences {width: auto; min-width: 700px; margin-left: 20px;}",
"#counts { width: auto; align: 'left'}",
".space { margin-right: 12px;}",
"p {margin: 0px;}",
"</style>",
'<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.0/jquery.min.js"></script>',
"<script>",
'$(document).ready(function(){',
"var currentMousePos = { x: -1, y: -1};",
'$("#sequences").html(function(i,el) {',
"return el.replace(/((A|C|G|T|N|-){10})/g, '$1<span class=\"space\"></span>')",
".replace(/A/g, '<span style=\"color:green\">A</span>')",
".replace(/C/g, '<span style=\"color:orange\">C</span>')",
".replace(/G/g, '<span style=\"color:red\">G</span>')",
".replace(/T/g, '<span style=\"color:blue\">T</span>')",
".replace(/U/g, '<span style=\"color:blue\">U</span>');",
'});',
"});",
"</script>",
"</head><body>",
"<h1>Enhancer homologs multiple alignments</h1>",
"<div id='align'>",
"<div id='seqnames'>", x100_n, "</div>",
"<div id='sequences'>", x100, "</div>",
"<div id='counts'>", counter, "</div>",
"</div></body></html>")
writeLines(html, filepath)
}
#' @importFrom Biostrings consensusMatrix DNAStringSet write.phylip
#' matchPattern alphabetFrequency injectHardMask
#' @importFrom IRanges IRangesList Views
#' @importFrom utils write.csv
saveAln <- function (x, filepath, motifConsensus, format) {
stopifnot("input must be an object of MultipleAlignment"=
inherits(x, "MultipleAlignment"))
checkMotifCons(motifConsensus)
## get consensus
enhancer <- strsplit(as.character(x@unmasked[1]), "")[[1]]
cons <- consensusMatrix(x, baseOnly=TRUE)
consid <- apply(cons[rownames(cons) %in% c("A", "C", "G", "T"), ,
drop=FALSE], 2, which.max)
consid[apply(cons[rownames(cons) %in% c("A", "C", "G", "T"), ,
drop=FALSE], 2, max)<2] <-
which(!rownames(cons) %in% c("A", "C", "G", "T"))[1]
cons <- rownames(cons)[consid]
cons[cons!=enhancer] <- "-"
cons <- paste(cons, collapse = "")
cons_m <- gsub("-", "N", cons)
cons <- DNAStringSet(cons)
names(cons) <- "Consensus"
x@unmasked <- c(x@unmasked, cons)
## search binding sites
if(length(motifConsensus)){
mt <- lapply(motifConsensus, function(.ele)
matchPattern(pattern = .ele, subject = cons_m))
mt <- mt[lengths(mt)>0]
mt <- unlist(IRangesList(mt))
involved_motifs <- sort(mt)
mt <- reduce(mt)
if(length(mt)){
m <- Views(cons_m, start = start(mt), end = end(mt))
m <- injectHardMask(m, letter="-")
m <- DNAStringSet(m)
names(m) <- "motifConsensus"
x@unmasked <- c(x@unmasked, m)
write.csv(involved_motifs, file = paste0(sub(paste0(".",format,"$"),
"", filepath),
".motifConsensus.info.csv"),
row.names=FALSE)
}
}
if(format=="txt"){
write.phylip(x, filepath = filepath)
}else{
write.phylip_html(x, filepath = filepath)
}
}
#' output alignments
#' @description Save enhancer homologs to file in phylip format.
#' @param al output of \link{alignment}.
#' @param output_folder output folder.
#' @param motifConsensus Transcription factor binding consensus.
#' @param format The format of output files.
#' Available formats are 'txt' and 'html'. Default is 'txt'.
#' @export
#' @return The I/O status.
#' @examples
#' al <- readRDS(system.file("extdata", "al.rds",
#' package="enhancerHomologSearch"))
#' tmpfolder <- tempdir()
#' library(MotifDb)
#' motifs <- query(MotifDb, "JASPAR_CORE")
#' consensus <- sapply(motifs, consensusString)
#' consensus <- DNAStringSet(gsub("\\?", "N", consensus))
#' saveAlignments(al, output_folder=tmpfolder, motifConsensus=consensus)
saveAlignments <- function(al,
output_folder=tempdir(),
motifConsensus=NULL,
format=c("txt", "html")){
checkMotifCons(motifConsensus)
format <- match.arg(format)
if(!file.exists(output_folder)){
dir.create(output_folder)
}
if(length(names(al))!=length(al)){
names(al) <- paste0("aln", seq_along(al), ".phylip.", format)
}else{
names(al) <- paste0(names(al), ".phylip.", format)
}
null <- mapply(saveAln, x=al,
filepath = file.path(output_folder, names(al)),
MoreArgs=list(motifConsensus = motifConsensus,
format=format))
return(invisible(null))
}
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