Nothing
writeResultsHTML <- function(resultsMEET, fileName='index.html') {
require("MEET")
require("seqinr")
require("seqLogo")
results <- resultsMEET$Results
fileName <- 'index.html'
iicc<-new.env()
switch(resultsMEET$Summary$organism,
"Rattus norvegicus"= switch(resultsMEET$Summary$method,
"Entropy"=data(RattusEntropy, envir=iicc),
"Divergence"=data(RattusDivergence, envir=iicc),
"Qresiduals"=data(RattusQresiduals, envir=iicc),
stop("Method not included")),
"Mus musculus"= switch(resultsMEET$Summary$method,
"Entropy"=data(MusEntropy, envir=iicc),
"Divergence"=data(MusDivergence, envir=iicc),
"Qresiduals"=data(MusQresiduals, envir=iicc),
stop("Method not included")),
"Drosophila melanogaster"= switch(resultsMEET$Summary$method,
"Entropy"=data(DrosophilaEntropy, envir=iicc),
"Divergence"=data(DrosophilaDivergence, envir=iicc),
"Qresiduals"=data(DrosophilaQresiduals, envir=iicc),
stop("Method not included")),
"Homo sapiens"= switch(resultsMEET$Summary$method,
"Entropy"=data(HomoEntropy, envir=iicc),
"Divergence"=data(HomoDivergence, envir=iicc),
"Qresiduals"=data(HomoQresiduals, envir=iicc),
stop("Method not included")),
stop("Organism not included"))
filename <- "NoLogo"
if (summary(paste("iicc", resultsMEET$Summary$nameTF,sep="")==ls(envir=iicc))[3]=="1") {
assign("TF",get(paste("iicc",resultsMEET$Summary$nameTF,sep=""),envir=iicc)$Transcriptionfactor)
filename <- paste(fileName,".png",sep="")
png(filename, bg = "transparent")
seqLogo(con(TF,method="profile")/nrow(TF))
dev.off()
}
pathMEET<-system.file(package="MEET")
file.copy(paste(paste(pathMEET,"exec",sep="/"), "LogoMEET.png",sep="/"),"LogoMEET.png",overwrite=TRUE)
sink(fileName)
cat(c('<!doctype html><html><head><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /><title>WebMEET: A web of Multiple Detection of Transcription Factor Binding Sites</title>'), sep="\n")
# webMEET.css
cat(c('<style type="text/css">', readLines(paste(paste(pathMEET,"exec",sep="/"), "webmeet.css",sep="/"),encoding="UTF-8"), '</style>'), sep="\n")
# jquery-ui-1.8.20.custom.css
cat(c('<style type="text/css">', readLines(paste(paste(pathMEET,"exec",sep="/"), "jquery-ui-1.8.20.custom.css",sep="/"),encoding="UTF-8"), '</style>'), sep="\n")
# jquery.cluetip.css paste(paste(pathMEET,"exec",sep="/"), "jquery.cluetip.css",sep="/")
cat(c('<style type="text/css">', readLines(paste(paste(pathMEET,"exec",sep="/"), "jquery.cluetip.css",sep="/"),encoding="UTF-8"), '</style>'), sep="\n")
# javascript
jsArray <- 'var result = new Array('
lines <- paste(paste(sapply(1:nrow(results), function(x) {
paste('{"Position":"', results[x,1], '","Value":"', results[x,2], '","Direction":"', results[x,3], '","Sequence":"', results[x,4], '","Organism":"', resultsMEET$Summary$organism, '","TF":"', resultsMEET$Summary$nameTF, '"}', sep='')
})), collapse=",")
jsArray <- paste(jsArray, lines, ');', sep='')
cat(c('<script type="text/javascript">', jsArray, '</script>'), sep='')
# jQuery.js
cat(c('<script type="text/javascript">', readLines(paste(paste(pathMEET,"exec",sep="/"), "jquery.js",sep="/"),encoding="UTF-8"), '</script>'), sep='\n')
cat(c('<script type="text/javascript">', readLines(paste(paste(pathMEET,"exec",sep="/"), "jquery-ui-1.8.20.custom.min.js",sep="/"),encoding="UTF-8"), '</script>'), sep='\n')
# jquery.cluetip.js
cat(c('<script type="text/javascript">', readLines(paste(paste(pathMEET,"exec",sep="/"), "jquery.cluetip.js",sep="/"),encoding="UTF-8"), '</script>'), sep='\n')
# webMEET.js
cat(c('<script type="text/javascript">', readLines(paste(paste(pathMEET,"exec",sep="/"), "webmeet.js",sep="/"),encoding="UTF-8"),'</script>'), sep='')
cat(c('</head><body><div id="main" class="inside"><div class="top_menu"><div class="logo"></div></div><div class="container">'), sep="\n")
cat(c('<div class="tableContainer"><table id="result" class="tablesorter" cellspacing="1" cellpadding="0" border="0"><thead><tr><th class="header">Sequence</th><th class="header">p-value</th><th class="header">Position</th><th class="header">Direction</th></tr></thead><tbody class="scrollContent">'), sep="\n")
cat(c('</tbody></table></div>'), sep="\n")
cat(c('<span id="sequence_result" class="letter" style="display: inline;">', paste(sapply(1:length(resultsMEET$Summary$DNA[[1]]), function(i) {
letter <- resultsMEET$Summary$DNA[[1]][i]
if (i %in% results[,1]) {
pos <- match(i, results[,1])
letter <- paste("<span id=\"", results[pos,4], results[pos,1], results[pos,3], "\" class=\"mark\" title=\"|<span class=\'tit\'>Organism:</span> <span class=\'res\'>", resultsMEET$Summary$organism, "</span>|<span class=\'tit\'>TF:</span> <span class=\'res\'>", resultsMEET$Summary$nameTF, "</span>|<span class=\'tit\'>Sequence:</span> <span class=\'res\'>", results[pos,4], "</span>|<span class=\'tit\'>p-value:</span> <span class=\'res\'>", results[pos, 2], "</span>|<span class=\'tit\'>Position:</span> <span class=\'res\'>", results[pos, 1], "</span>|<span class=\'tit\'>Direction:</span> <span class=\'res\'>", results[pos, 3], "\"</span>", letter, "</span>", sep='')
}
if (i %% 60 == 0) {
paste(letter, '\n', sep='')
} else {
letter
}
}), collapse=''), '</span>'), sep='\n')
cat(c('</div></div><div id="dialog" title="Basic dialog"><img id="consensus" src="', filename, '" style="width:350px" /></div></body></html>'))
sink()
# browseURL(paste('file:///', getwd(), fileName, sep='/'))
}
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