Nothing
R/output.R
In ddCt: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Defines functions
writeSimpleTabCsv
writeLines.ddCt
xtable.ddCt
Documented in
writeSimpleTabCsv
################################################################################
##
## This software is created by Molecular Genom Analysis Group
## Department of German Cancer Research Center in Heidelberg
##
##
## output.R
## Created on: Oct 23, 2008
## Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de>
## Description: Output utility
##
################################################################################
## xtable method
## TODO: change S3 methods from "ddCt" to "ddCtExpression"
xtable.ddCt <- function(expSet,name="exprs",na.threshold,...) {
ad <- assayData(expSet)
if(missing(name))
name <- "exprs"
if(!name %in% names(ad))
stop("Data entry '", name,"' not found! It should be of the following:\n\t",
paste(names(ad), collapse=","),"\n")
pos <- match(name,names(ad))
nas <- t(ad$numberNA)
numbers <- t(ad$number)
exp <- t(ad[[pos]])
if(!missing(na.threshold)) {
if(!is.numeric(na.threshold)) {stop("'na.threshold' must be numeric!\n")}
if(na.threshold >100 | na.threshold < 0) {
stop ("'na.threshold' must range between 0 and 100 - as percentage!\n")
}
highna <- nas >= numbers * na.threshold / 100
exp[highna] <- NA
}
xtable(exp,...)
}
## write ddCt into file
writeLines.ddCt <- function(expSet, con=stdout(),sep="\n",type="html",name="exprs",...) {
txt <- print(xtable.ddCt(expSet,
xname=name,...),type=type)
writeLines(txt, con=con,sep=sep)
}
## write tab-delimited, not quoted and no-row-name TSV files
writeSimpleTabCsv <- function(x, file="",...) {
Call <- match.call(expand.dots=TRUE)
for(argname in c("row.names", "sep", "quote")) {
if (!is.null(Call[[argname]]))
warning(gettextf("attemp to set '%s' ignored", argname), domain=NA)
}
Call$row.names <- FALSE
Call$sep <- "\t"
Call$quote <- FALSE
Call[[1L]] <- as.name("write.table")
eval.parent(Call)
}
## write html table, contributed by Andreas Buness
##------------------------------------------------------------
## writes a html table
## x: data frame
## filename: character with the name of the output file
## sortby: name of a column in data frame din
##------------------------------------------------------------
write.htmltable <- function (x, file, title="", sortby=NULL, decreasing=TRUE, open="wt") {
if(!is.null(sortby)) {
if(!sortby %in% colnames(x))
stop(paste("Invalid argument \"sortby\": could not find a column in data frame x with name", sortby))
soby = x[, sortby]
if(!is.numeric(soby))
stop("Invalid argument \"sortby\": column is not numeric")
x = x[order(soby, decreasing=decreasing), ]
}
outfile <- file(paste(file, ".html", sep=""), open=open)
cat("<html>", "<STYLE>",
"<!--TD { FONT-FAMILY: Helvetica,Arial; FONT-SIZE: 14px;}-->",
"<!--H1 { FONT-FAMILY: Helvetica,Arial; FONT-SIZE: 22px;}-->",
"</STYLE>", "<head>", paste("<TITLE>", title, "</TITLE>", sep=""),
"</head>", "<body bgcolor=#ffffff>", file = outfile, sep = "\n")
if (title!="")
cat("<CENTER><H1 ALIGN=\"CENTER\">", title, " </H1></CENTER>\n",
file = outfile, sep = "\n")
cat("<CENTER> \n", file = outfile)
cat("<TABLE BORDER=0>", file = outfile, sep = "\n")
cat("<TR>", file = outfile)
for (j in 1:ncol(x))
cat("<TD BGCOLOR=\"", c("#e0e0ff", "#d0d0f0")[j%%2+1], "\"><B>", colnames(x)[j], "</B></TD>\n", sep="", file = outfile)
cat("</TR>", file = outfile)
for (i in 1:nrow(x)) {
cat("<TR>", file = outfile)
for (j in 1:ncol(x)) {
txt <- as.character(x[i,j])
if (length(grep("^http:", txt))>0) {
txt <- sub(";$", "", txt) ## remove trailing semicolon
s <- unlist(strsplit(txt, "[/?=]")) ## split out last part of URL
txt <- paste("<A HREF=\"", txt, "\" TARGET=\"z\">", s[length(s)], "</A>", sep="")
}
cat("<TD BGCOLOR=\"", c("#e0e0ff", "#d0d0f0", "#f0f0ff", "#e0e0f0")[i%%2*2+j%%2+1], "\">",
txt, "</TD>\n", sep="", file = outfile)
}
cat("</TR>", file = outfile)
}
cat("</TABLE></CENTER>", "</body>", "</html>", sep = "\n", file = outfile)
close(outfile)
}
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ddCt documentation built on Nov. 8, 2020, 4:57 p.m.
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Defines functions writeSimpleTabCsv writeLines.ddCt xtable.ddCt
Documented in writeSimpleTabCsv
################################################################################
##
## This software is created by Molecular Genom Analysis Group
## Department of German Cancer Research Center in Heidelberg
##
##
## output.R
## Created on: Oct 23, 2008
## Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de>
## Description: Output utility
##
################################################################################
## xtable method
## TODO: change S3 methods from "ddCt" to "ddCtExpression"
xtable.ddCt <- function(expSet,name="exprs",na.threshold,...) {
ad <- assayData(expSet)
if(missing(name))
name <- "exprs"
if(!name %in% names(ad))
stop("Data entry '", name,"' not found! It should be of the following:\n\t",
paste(names(ad), collapse=","),"\n")
pos <- match(name,names(ad))
nas <- t(ad$numberNA)
numbers <- t(ad$number)
exp <- t(ad[[pos]])
if(!missing(na.threshold)) {
if(!is.numeric(na.threshold)) {stop("'na.threshold' must be numeric!\n")}
if(na.threshold >100 | na.threshold < 0) {
stop ("'na.threshold' must range between 0 and 100 - as percentage!\n")
}
highna <- nas >= numbers * na.threshold / 100
exp[highna] <- NA
}
xtable(exp,...)
}
## write ddCt into file
writeLines.ddCt <- function(expSet, con=stdout(),sep="\n",type="html",name="exprs",...) {
txt <- print(xtable.ddCt(expSet,
xname=name,...),type=type)
writeLines(txt, con=con,sep=sep)
}
## write tab-delimited, not quoted and no-row-name TSV files
writeSimpleTabCsv <- function(x, file="",...) {
Call <- match.call(expand.dots=TRUE)
for(argname in c("row.names", "sep", "quote")) {
if (!is.null(Call[[argname]]))
warning(gettextf("attemp to set '%s' ignored", argname), domain=NA)
}
Call$row.names <- FALSE
Call$sep <- "\t"
Call$quote <- FALSE
Call[[1L]] <- as.name("write.table")
eval.parent(Call)
}
## write html table, contributed by Andreas Buness
##------------------------------------------------------------
## writes a html table
## x: data frame
## filename: character with the name of the output file
## sortby: name of a column in data frame din
##------------------------------------------------------------
write.htmltable <- function (x, file, title="", sortby=NULL, decreasing=TRUE, open="wt") {
if(!is.null(sortby)) {
if(!sortby %in% colnames(x))
stop(paste("Invalid argument \"sortby\": could not find a column in data frame x with name", sortby))
soby = x[, sortby]
if(!is.numeric(soby))
stop("Invalid argument \"sortby\": column is not numeric")
x = x[order(soby, decreasing=decreasing), ]
}
outfile <- file(paste(file, ".html", sep=""), open=open)
cat("<html>", "<STYLE>",
"<!--TD { FONT-FAMILY: Helvetica,Arial; FONT-SIZE: 14px;}-->",
"<!--H1 { FONT-FAMILY: Helvetica,Arial; FONT-SIZE: 22px;}-->",
"</STYLE>", "<head>", paste("<TITLE>", title, "</TITLE>", sep=""),
"</head>", "<body bgcolor=#ffffff>", file = outfile, sep = "\n")
if (title!="")
cat("<CENTER><H1 ALIGN=\"CENTER\">", title, " </H1></CENTER>\n",
file = outfile, sep = "\n")
cat("<CENTER> \n", file = outfile)
cat("<TABLE BORDER=0>", file = outfile, sep = "\n")
cat("<TR>", file = outfile)
for (j in 1:ncol(x))
cat("<TD BGCOLOR=\"", c("#e0e0ff", "#d0d0f0")[j%%2+1], "\"><B>", colnames(x)[j], "</B></TD>\n", sep="", file = outfile)
cat("</TR>", file = outfile)
for (i in 1:nrow(x)) {
cat("<TR>", file = outfile)
for (j in 1:ncol(x)) {
txt <- as.character(x[i,j])
if (length(grep("^http:", txt))>0) {
txt <- sub(";$", "", txt) ## remove trailing semicolon
s <- unlist(strsplit(txt, "[/?=]")) ## split out last part of URL
txt <- paste("<A HREF=\"", txt, "\" TARGET=\"z\">", s[length(s)], "</A>", sep="")
}
cat("<TD BGCOLOR=\"", c("#e0e0ff", "#d0d0f0", "#f0f0ff", "#e0e0f0")[i%%2*2+j%%2+1], "\">",
txt, "</TD>\n", sep="", file = outfile)
}
cat("</TR>", file = outfile)
}
cat("</TABLE></CENTER>", "</body>", "</html>", sep = "\n", file = outfile)
close(outfile)
}
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