Nothing
R/PKoutput.R
In PKreport: A reporting pipeline for checking population pharmacokinetic model assumption
Defines functions
match.index
writeHTML
writeTable
writeLst
writeLst.tab
PKoutput
Documented in
PKoutput
#############################################################################################
## File: PKoutput.R
## Author: Xiaoyong Sun
## Date: 10/12/2009
## Goal: PKoutput
## Notes:
## -
#############################################################################################
## user should not use this function
## match lattice figure against ggplot figure to output both figure parallel
# input: - lattice.note: figure note
# - ggplot.note: figure note
# output: vector index for ggplot.note that matches lattice.note
match.index <- function(lattice.note, ggplot.note)
{
tmp.lattice.list <- strsplit(lattice.note, "lattice")
tmp.ggplot.list <- strsplit(ggplot.note, "ggplot2")
tmp.lattice <- unlist(tmp.lattice.list)
rm.index <- which(tmp.lattice==")")
tmp.lattice <- tmp.lattice[-rm.index]
tmp.ggplot <- unlist(tmp.ggplot.list)
rm.index <- which(tmp.ggplot==")")
tmp.ggplot <- tmp.ggplot[-rm.index]
ggplot.index <- match(tmp.lattice, tmp.ggplot)
return(ggplot.index)
}
# Create fig file with html directory from input and fig format from input
# - input: 1. the html directory to keep figures
# 2. the save format for figures, in order to find the matching figs in the folder
# - output: a html file with figures
writeHTML <- function(htmldir, save.format)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.start <- paste(html.start, "<title>PKoutput", htmldir, "Figures</title></header><body>",
sep=" ")
html.start <- paste(html.start, "<hr><h3><p class=\"subtitle\">", htmldir,
"Figures</p></h3>", sep=" ")
html.content <- NULL
fig.files <- dir(htmldir, pattern=save.format)
fig.files <- paste(htmldir, fig.files, sep="/")
txt <- paste("<img src=", fig.files, sep="")
txt <- paste(txt, ">", sep="")
# lattice package
if (.pkplot$getConfig("package")==0)
{
lattice.txt <- txt[grep("lattice", txt)]
lattice.no <- sapply(1:length(lattice.txt), function(i) strsplit(lattice.txt[i], "_")[[1]][2])
lattice.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(lattice.no))]
lattice.note <- unlist(lattice.note)
# add content
# html.content: Notes for figures
# html.body: figures
# html code: 1. html.content; 2. html.body
html.tmp <- paste("<a href=\"#", lattice.no, "\">", lattice.note, "</a>", sep="")
html.tmp <- paste("<td>", html.tmp, "</td>", sep="")
## every 4 contents in one row
# add <tr>
tr.index <- which((((1:length(lattice.note))-1)%%4) == 0)
html.tmp[tr.index] <- paste("<tr>", html.tmp[tr.index], sep="")
# add </tr>
tr.index <- which(((1:length(lattice.note))%%4) == 0)
html.tmp[tr.index] <- paste(html.tmp[tr.index], "</tr>", sep="")
html.content <- paste(html.content, html.tmp, collapse="")
html.content <- paste("<a name=\"top\"><h3><table cellpadding=5 align=center>", html.content, "</table></h3></a>", sep="")
title.body <- "<p><center><h2>Lattice package</h2></center></p>"
fig.tmp <- paste("<a name=\"", lattice.no, "\">", lattice.no, "</a>", sep="")
fig.body <- paste("<p>Figure ID: ", fig.tmp, "</p><a href=\"#top\">Top</a>", sep="")
fig.body <- paste(fig.body, "<p> Note: ", lattice.note, "</p>", sep="")
fig.body <- paste(fig.body, lattice.txt, collapse="")
html.body <- paste(title.body, fig.body, sep="")
}
## ggplot package
if (.pkplot$getConfig("package")==1)
{
ggplot.txt <- txt[grep("ggplot", txt)]
if (length(ggplot.txt) > 0)
{
ggplot.no <- sapply(1:length(ggplot.txt), function(i) strsplit(ggplot.txt[i], "_")[[1]][2])
ggplot.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(ggplot.no))]
ggplot.note <- unlist(ggplot.note)
# add content
html.tmp <- paste("<a href=\"#", ggplot.no, "\">", ggplot.note, "</a>", sep="")
html.tmp <- paste("<td>", html.tmp, "</td>", sep="")
## every 4 contents in one row
# add <tr>
tr.index <- which((((1:length(ggplot.note))-1)%%4) == 0)
html.tmp[tr.index] <- paste("<tr>", html.tmp[tr.index], sep="")
# add </tr>
tr.index <- which(((1:length(ggplot.note))%%4) == 0)
html.tmp[tr.index] <- paste(html.tmp[tr.index], "</tr>", sep="")
html.content <- paste(html.content, html.tmp, collapse="")
html.content <- paste("<a name=\"top\"><h3><table cellpadding=5 align=center>", html.content, "</table></h3></a>", sep="")
title.body <- "<p><center><h2>ggplot package</h2></center></p>"
fig.tmp <- paste("<a name=\"", ggplot.no, "\">", ggplot.no, "</a>", sep="")
fig.body <- paste("<p>Figure ID: ", fig.tmp, "</p><a href=\"#top\">Top</a>", sep="")
fig.body <- paste(fig.body, "<p> Note: ", ggplot.note, "</p>", sep="")
fig.body <- paste(fig.body, ggplot.txt, collapse="")
html.body <- paste(title.body, fig.body, sep="")
}
}
if (.pkplot$getConfig("package")==2)
{
lattice.txt <- txt[grep("lattice", txt)]
ggplot.txt <- txt[grep("ggplot", txt)]
if (length(lattice.txt)==0) stop("There is no lattice figure!")
if (length(ggplot.txt)==0) stop("There is no ggplot figure!")
lattice.no <- sapply(1:length(lattice.txt), function(i) strsplit(lattice.txt[i], "_")[[1]][2])
lattice.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(lattice.no))]
lattice.note <- unlist(lattice.note)
ggplot.no <- sapply(1:length(ggplot.txt), function(i) strsplit(ggplot.txt[i], "_")[[1]][2])
ggplot.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(ggplot.no))]
ggplot.note <- unlist(ggplot.note)
ggplot.index <- match.index(lattice.note, ggplot.note)
ggplot.txt <- ggplot.txt[ggplot.index]
ggplot.note <- ggplot.note[ggplot.index]
ggplot.no <- ggplot.no[ggplot.index]
# add content
# html.content: Notes table for figures
# html.body: figures
# html code: 1. html.content; 2. html.body
lattice.note.1 <- strsplit(lattice.note, " \\(")
lattice.note.2 <- unlist(lattice.note.1)
tmp.index <- which(lattice.note.2 == "lattice)")
lattice.note.3 <- lattice.note.2[-tmp.index]
html.tmp <- paste("<a href=\"#", lattice.no, "\">", lattice.note.3, "</a>", sep="")
html.tmp <- paste("<td>", html.tmp, "</td>", sep="")
## every 4 contents in one row
# add <tr>
trs.index <- which((((1:length(lattice.note))-1)%%4) == 0)
html.tmp[trs.index] <- paste("<tr>", html.tmp[trs.index], sep="")
# add </tr>
tre.index <- which(((1:length(lattice.note))%%4) == 0)
html.tmp[tre.index] <- paste(html.tmp[tre.index], "</tr>", sep="")
html.content <- paste(html.content, html.tmp, collapse="")
# control last component
if (length(trs.index) != length(tre.index)) html.content <- paste(html.content, "</tr>", sep="")
html.content <- paste("<a name=\"top\"><h3><table class=\"figcenter\">", html.content, "</table></h3></a>", sep="")
# setup 'figure id'
fig.tmp.lattice <- paste("<a name=\"", lattice.no, "\">", lattice.no, "</a>", sep="")
fig.id.lattice <- paste("<td>Figure ID: ", fig.tmp.lattice, "<a href=\"#top\"> Top </a></td>", sep="")
fig.id.ggplot <- paste("<td>Figure ID: ", ggplot.no, "</td>", sep="")
fig.id <- paste("<tr>", fig.id.lattice, fig.id.ggplot, "</tr>", sep="")
# setup 'figure.note'
fig.note.lattice <- paste("<td> Note: ", lattice.note, "</td>", sep="")
fig.note.ggplot <- paste("<td> Note: ", ggplot.note, "</td>", sep="")
fig.note <- paste("<tr>", fig.note.lattice, fig.note.ggplot, "</tr>", sep="")
# setup 'figure'
fig.fig.lattice <- paste("<td>", lattice.txt, "</td>", sep="")
fig.fig.ggplot <- paste("<td>", ggplot.txt, "</td>", sep="")
fig.fig <- paste("<tr>", fig.fig.lattice, fig.fig.ggplot, "</tr>", sep="")
fig.body <- paste(fig.id, fig.note, fig.fig, sep="")
fig.body <- paste(fig.body, collapse="")
fig.body <- paste("<table class=\"center\">", fig.body, "</table>", sep="")
title.body <- "<p><center><h2>lattice and ggplot package</h2></center></p>"
html.body <- paste(title.body, fig.body, sep="")
}
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
filename <- paste("PK", htmldir, ".html", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.body, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
# Create file with file name from input and content from input
# - input: 1. the html filename you want to creat
# 2. the title of html file
# 2. the content as a table
# - output: a html file
writeTable <- function(filename, mytitle, mydata)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
# generate data file
html.start<- paste(html.start, "<title>", mytitle,
"</title></header><body>", sep=" ")
html.start <- paste(html.start, "<hr><h3><p class=\"subtitle\">", mytitle,
"Table</p></h3>", sep=" ")
## Add description
html.content <- paste("<h4>Color Description (scaled in column direction)</h4>", sep="")
html.content <- paste(html.content,
"<table><tr><td BGCOLOR= #33FFFF>25%</td><td BGCOLOR= #FFFF99>50%</td><td BGCOLOR= #FFCC00>75%</td><td BGCOLOR= #FF6600>100%</td></tr></table>", sep="")
html.content <- paste(html.content, "<h4>Data</h4><table>", sep="")
html.colname <- paste("<td BGCOLOR= #66FF66>", colnames(mydata), "</td>", sep="", collapse="")
html.content <- paste(html.content, "<tr>", html.colname, "</tr>", sep="")
html.data <- NULL
for (i in 1:ncol(mydata))
{
tmp <- mydata[,i]
if (length(unique(tmp))>=5 && is.numeric(tmp))
{
order.index <- order(as.numeric(tmp))
# TODO: have more color choice?
quantile.index <- round(quantile(1:length(order.index), c(0.25,0.5,0.75)))
# q25, 50, 75, 100
q25.index <- c(1:quantile.index[1])
if (quantile.index[1]!=quantile.index[2]) q50.index <- c((quantile.index[1]+1):quantile.index[2])
if (quantile.index[2]!=quantile.index[3]) q75.index <- c((quantile.index[2]+1):quantile.index[3])
if (quantile.index[3] < length(order.index)) q100.index <- c((quantile.index[3]+1):(length(order.index)))
tmp[order.index[q25.index]] <- paste("<td BGCOLOR= #33FFFF>", tmp[order.index[q25.index]], "</td>", sep="")
tmp[order.index[q50.index]] <- paste("<td BGCOLOR= #FFFF99>", tmp[order.index[q50.index]], "</td>", sep="")
tmp[order.index[q75.index]] <- paste("<td BGCOLOR= #FFCC00>", tmp[order.index[q75.index]], "</td>", sep="")
tmp[order.index[q100.index]] <- paste("<td BGCOLOR= #FF6600>", tmp[order.index[q100.index]], "</td>", sep="")
}
else
{
if (length(unique(tmp)) >=3 && is.numeric(tmp))
{
#min
min.index <- which(tmp==min(tmp))
max.index <- which(tmp==max(tmp))
tmp[min.index] <- paste("<td BGCOLOR= #33FFFF>", tmp[min.index], "</td>", sep="")
tmp[max.index] <- paste("<td BGCOLOR= #FF6600>", tmp[max.index], "</td>", sep="")
tmp[-c(min.index, max.index)] <- paste("<td>", tmp[-c(min.index, max.index)], "</td>", sep="")
}
else
{
tmp <- paste("<td>", tmp, "</td>", sep="")
}
}
mydata[,i] <- tmp
}
for (i in 1:nrow(mydata))
{
html.data <- paste(mydata[i,], sep="", collapse="")
html.content <- paste(html.content, "<tr>", html.data, "</tr>", sep="")
}
html.content <- paste(html.content, "</table>", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
# Create file with file name from input and content from input
# - input: 1. the html filename you want to creat
# 2. the content as a string
# - output: a html file
writeLst <- function(filename, lstString)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
# generate data file
#browser()
html.start<- paste(html.start, "<title>lst file",
"</title></header><body>", sep=" ")
html.start <- paste(html.start, "<hr><h3><p class=\"subtitle\">lst file</p></h3>", sep=" ")
html.content <- paste(lstString, "<br>", sep="")
html.content <- paste(html.content, collapse="")
html.content <- paste("<p><pre>", html.content, "</pre></p>", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
writeLst.tab <- function(filename, lstString)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
# generate data file
html.start<- paste(html.start, "<title>lst file",
"</title></header><body>", sep=" ")
html.content <- "<table>"
for (i in 1:length(lstString))
{
tmp <- strsplit(lstString[i], " ")[[1]]
tmp.html <- paste(tmp, collapse="</td><td>")
html.content <- paste(html.content, "<tr><td>", tmp.html, "</td></tr>", sep="")
}
html.content <- paste(html.content, "</table>", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
PKoutput <- function(nonmemObj=NULL, table.Rowv=FALSE, table.Colv=FALSE)
{
general.list <- .pkplot$getGlobalConfig()
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", "PKreport.css", package="PKreport"),
"http://129.186.62.12/PKreport.css",
#"PKreport.css",
"\"/>", sep="")
html.index <- paste(html.start, "<title>PKreport</title></header><body>", sep="")
## add symbol image
html.index <- paste(html.index, "<h1><p class=\"title\">PKreport</p></h1>", sep="")
## general output
if ((!is.null(nonmemObj)) && class(nonmemObj) == "nonmem")
{
# start table
html.index <- paste(html.index,
"<h3><p class=\"subtitle\">NONMEM results</p></h3><table class=\"center\" border=0>",
sep="")
# lst file
if (length(nonmemObj@file.lst) != 0)
{
writeLst("lst.html", nonmemObj@file.lst)
html.index <- paste(html.index, "<tr><td><a href=lst.html>lst file</a></td></tr>", sep="")
}
# tab file, match that in "nonmem" class
if (nrow(nonmemObj@tabdata) != 0)
{
order.data <- nonmemObj@tabdata
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("tab.html", "tab file", order.data)
html.index <- paste(html.index, "<tr><td><a href=tab.html>Tab file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.cov$data) != 0)
{
order.data <- nonmemObj@file.cov$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("cov.html", "cov file",order.data)
html.index <- paste(html.index, "<tr><td><a href=cov.html>Cov file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.cor$data) != 0)
{
order.data <- nonmemObj@file.cor$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("cor.html", "cor file",order.data)
html.index <- paste(html.index, "<tr><td><a href=cor.html>Cor file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.coi$data) != 0)
{
order.data <- nonmemObj@file.coi$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("coi.html", "coi file",order.data)
html.index <- paste(html.index, "<tr><td><a href=coi.html>Coi file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.phi$data) != 0)
{
order.data <- nonmemObj@file.phi$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("phi.html", "phi file",order.data)
html.index <- paste(html.index, "<tr><td><a href=phi.html>phi file</a></td></tr>", sep="")
}
}
#########################
## add separator
#########################
html.index <- paste(html.index, "</table><hr><h3><p class=\"subtitle\">Diagnostics</p></h3><table class=\"center\" border=0>", sep="")
## univariate figures
if (file.exists(general.list$univar.dir))
{
writeHTML(general.list$univar.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKunivar.html>Univariate Figures</a></td></tr>", sep="")
}
## bivariate figures
if (file.exists(general.list$bivar.dir))
{
writeHTML(general.list$bivar.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKbivar.html>Bivariate Figures</a></td></tr>", sep="")
}
## bivariate figures
if (file.exists(general.list$ind.dir))
{
writeHTML(general.list$ind.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKind.html>Individual Figures</a></td></tr>", sep="")
}
## gof figures
if (file.exists(general.list$gof.dir))
{
writeHTML(general.list$gof.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKgof.html>Figures for Goodness of Fit</a></td></tr>", sep="")
}
if (file.exists(general.list$struct.dir))
{
writeHTML(general.list$struct.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKstruct.html>Figures for Structural Model Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$resid.dir))
{
writeHTML(general.list$resid.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKresid.html>Figures for Residual Model Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$para.dir))
{
writeHTML(general.list$para.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKpara.html>Figures for Parameters Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$cov.dir))
{
writeHTML(general.list$cov.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKcov.html>Figures for Covariate Model Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$eta.dir))
{
writeHTML(general.list$eta.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKeta.html>Figures for Random Effects Dagnostics</a></td></tr>", sep="")
}
if (file.exists("PKcode.txt"))
{
html.index <- paste(html.index, "<tr><td><a href=PKcode.txt>R Code for Figures</a></td></tr>", sep="")
}
# end table
html.index <- paste(html.index, "</table>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
html.index <- paste(html.index, html.end, sep="")
PK.html <- file("PKindex.html", "w") # open an output file connection
writeLines(html.index, con = PK.html, sep = "\n")
close(PK.html)
}
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Defines functions match.index writeHTML writeTable writeLst writeLst.tab PKoutput
Documented in PKoutput
#############################################################################################
## File: PKoutput.R
## Author: Xiaoyong Sun
## Date: 10/12/2009
## Goal: PKoutput
## Notes:
## -
#############################################################################################
## user should not use this function
## match lattice figure against ggplot figure to output both figure parallel
# input: - lattice.note: figure note
# - ggplot.note: figure note
# output: vector index for ggplot.note that matches lattice.note
match.index <- function(lattice.note, ggplot.note)
{
tmp.lattice.list <- strsplit(lattice.note, "lattice")
tmp.ggplot.list <- strsplit(ggplot.note, "ggplot2")
tmp.lattice <- unlist(tmp.lattice.list)
rm.index <- which(tmp.lattice==")")
tmp.lattice <- tmp.lattice[-rm.index]
tmp.ggplot <- unlist(tmp.ggplot.list)
rm.index <- which(tmp.ggplot==")")
tmp.ggplot <- tmp.ggplot[-rm.index]
ggplot.index <- match(tmp.lattice, tmp.ggplot)
return(ggplot.index)
}
# Create fig file with html directory from input and fig format from input
# - input: 1. the html directory to keep figures
# 2. the save format for figures, in order to find the matching figs in the folder
# - output: a html file with figures
writeHTML <- function(htmldir, save.format)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.start <- paste(html.start, "<title>PKoutput", htmldir, "Figures</title></header><body>",
sep=" ")
html.start <- paste(html.start, "<hr><h3><p class=\"subtitle\">", htmldir,
"Figures</p></h3>", sep=" ")
html.content <- NULL
fig.files <- dir(htmldir, pattern=save.format)
fig.files <- paste(htmldir, fig.files, sep="/")
txt <- paste("<img src=", fig.files, sep="")
txt <- paste(txt, ">", sep="")
# lattice package
if (.pkplot$getConfig("package")==0)
{
lattice.txt <- txt[grep("lattice", txt)]
lattice.no <- sapply(1:length(lattice.txt), function(i) strsplit(lattice.txt[i], "_")[[1]][2])
lattice.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(lattice.no))]
lattice.note <- unlist(lattice.note)
# add content
# html.content: Notes for figures
# html.body: figures
# html code: 1. html.content; 2. html.body
html.tmp <- paste("<a href=\"#", lattice.no, "\">", lattice.note, "</a>", sep="")
html.tmp <- paste("<td>", html.tmp, "</td>", sep="")
## every 4 contents in one row
# add <tr>
tr.index <- which((((1:length(lattice.note))-1)%%4) == 0)
html.tmp[tr.index] <- paste("<tr>", html.tmp[tr.index], sep="")
# add </tr>
tr.index <- which(((1:length(lattice.note))%%4) == 0)
html.tmp[tr.index] <- paste(html.tmp[tr.index], "</tr>", sep="")
html.content <- paste(html.content, html.tmp, collapse="")
html.content <- paste("<a name=\"top\"><h3><table cellpadding=5 align=center>", html.content, "</table></h3></a>", sep="")
title.body <- "<p><center><h2>Lattice package</h2></center></p>"
fig.tmp <- paste("<a name=\"", lattice.no, "\">", lattice.no, "</a>", sep="")
fig.body <- paste("<p>Figure ID: ", fig.tmp, "</p><a href=\"#top\">Top</a>", sep="")
fig.body <- paste(fig.body, "<p> Note: ", lattice.note, "</p>", sep="")
fig.body <- paste(fig.body, lattice.txt, collapse="")
html.body <- paste(title.body, fig.body, sep="")
}
## ggplot package
if (.pkplot$getConfig("package")==1)
{
ggplot.txt <- txt[grep("ggplot", txt)]
if (length(ggplot.txt) > 0)
{
ggplot.no <- sapply(1:length(ggplot.txt), function(i) strsplit(ggplot.txt[i], "_")[[1]][2])
ggplot.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(ggplot.no))]
ggplot.note <- unlist(ggplot.note)
# add content
html.tmp <- paste("<a href=\"#", ggplot.no, "\">", ggplot.note, "</a>", sep="")
html.tmp <- paste("<td>", html.tmp, "</td>", sep="")
## every 4 contents in one row
# add <tr>
tr.index <- which((((1:length(ggplot.note))-1)%%4) == 0)
html.tmp[tr.index] <- paste("<tr>", html.tmp[tr.index], sep="")
# add </tr>
tr.index <- which(((1:length(ggplot.note))%%4) == 0)
html.tmp[tr.index] <- paste(html.tmp[tr.index], "</tr>", sep="")
html.content <- paste(html.content, html.tmp, collapse="")
html.content <- paste("<a name=\"top\"><h3><table cellpadding=5 align=center>", html.content, "</table></h3></a>", sep="")
title.body <- "<p><center><h2>ggplot package</h2></center></p>"
fig.tmp <- paste("<a name=\"", ggplot.no, "\">", ggplot.no, "</a>", sep="")
fig.body <- paste("<p>Figure ID: ", fig.tmp, "</p><a href=\"#top\">Top</a>", sep="")
fig.body <- paste(fig.body, "<p> Note: ", ggplot.note, "</p>", sep="")
fig.body <- paste(fig.body, ggplot.txt, collapse="")
html.body <- paste(title.body, fig.body, sep="")
}
}
if (.pkplot$getConfig("package")==2)
{
lattice.txt <- txt[grep("lattice", txt)]
ggplot.txt <- txt[grep("ggplot", txt)]
if (length(lattice.txt)==0) stop("There is no lattice figure!")
if (length(ggplot.txt)==0) stop("There is no ggplot figure!")
lattice.no <- sapply(1:length(lattice.txt), function(i) strsplit(lattice.txt[i], "_")[[1]][2])
lattice.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(lattice.no))]
lattice.note <- unlist(lattice.note)
ggplot.no <- sapply(1:length(ggplot.txt), function(i) strsplit(ggplot.txt[i], "_")[[1]][2])
ggplot.note <- .pkplot$getAllPKCodeNote()[c(as.numeric(ggplot.no))]
ggplot.note <- unlist(ggplot.note)
ggplot.index <- match.index(lattice.note, ggplot.note)
ggplot.txt <- ggplot.txt[ggplot.index]
ggplot.note <- ggplot.note[ggplot.index]
ggplot.no <- ggplot.no[ggplot.index]
# add content
# html.content: Notes table for figures
# html.body: figures
# html code: 1. html.content; 2. html.body
lattice.note.1 <- strsplit(lattice.note, " \\(")
lattice.note.2 <- unlist(lattice.note.1)
tmp.index <- which(lattice.note.2 == "lattice)")
lattice.note.3 <- lattice.note.2[-tmp.index]
html.tmp <- paste("<a href=\"#", lattice.no, "\">", lattice.note.3, "</a>", sep="")
html.tmp <- paste("<td>", html.tmp, "</td>", sep="")
## every 4 contents in one row
# add <tr>
trs.index <- which((((1:length(lattice.note))-1)%%4) == 0)
html.tmp[trs.index] <- paste("<tr>", html.tmp[trs.index], sep="")
# add </tr>
tre.index <- which(((1:length(lattice.note))%%4) == 0)
html.tmp[tre.index] <- paste(html.tmp[tre.index], "</tr>", sep="")
html.content <- paste(html.content, html.tmp, collapse="")
# control last component
if (length(trs.index) != length(tre.index)) html.content <- paste(html.content, "</tr>", sep="")
html.content <- paste("<a name=\"top\"><h3><table class=\"figcenter\">", html.content, "</table></h3></a>", sep="")
# setup 'figure id'
fig.tmp.lattice <- paste("<a name=\"", lattice.no, "\">", lattice.no, "</a>", sep="")
fig.id.lattice <- paste("<td>Figure ID: ", fig.tmp.lattice, "<a href=\"#top\"> Top </a></td>", sep="")
fig.id.ggplot <- paste("<td>Figure ID: ", ggplot.no, "</td>", sep="")
fig.id <- paste("<tr>", fig.id.lattice, fig.id.ggplot, "</tr>", sep="")
# setup 'figure.note'
fig.note.lattice <- paste("<td> Note: ", lattice.note, "</td>", sep="")
fig.note.ggplot <- paste("<td> Note: ", ggplot.note, "</td>", sep="")
fig.note <- paste("<tr>", fig.note.lattice, fig.note.ggplot, "</tr>", sep="")
# setup 'figure'
fig.fig.lattice <- paste("<td>", lattice.txt, "</td>", sep="")
fig.fig.ggplot <- paste("<td>", ggplot.txt, "</td>", sep="")
fig.fig <- paste("<tr>", fig.fig.lattice, fig.fig.ggplot, "</tr>", sep="")
fig.body <- paste(fig.id, fig.note, fig.fig, sep="")
fig.body <- paste(fig.body, collapse="")
fig.body <- paste("<table class=\"center\">", fig.body, "</table>", sep="")
title.body <- "<p><center><h2>lattice and ggplot package</h2></center></p>"
html.body <- paste(title.body, fig.body, sep="")
}
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
filename <- paste("PK", htmldir, ".html", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.body, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
# Create file with file name from input and content from input
# - input: 1. the html filename you want to creat
# 2. the title of html file
# 2. the content as a table
# - output: a html file
writeTable <- function(filename, mytitle, mydata)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
# generate data file
html.start<- paste(html.start, "<title>", mytitle,
"</title></header><body>", sep=" ")
html.start <- paste(html.start, "<hr><h3><p class=\"subtitle\">", mytitle,
"Table</p></h3>", sep=" ")
## Add description
html.content <- paste("<h4>Color Description (scaled in column direction)</h4>", sep="")
html.content <- paste(html.content,
"<table><tr><td BGCOLOR= #33FFFF>25%</td><td BGCOLOR= #FFFF99>50%</td><td BGCOLOR= #FFCC00>75%</td><td BGCOLOR= #FF6600>100%</td></tr></table>", sep="")
html.content <- paste(html.content, "<h4>Data</h4><table>", sep="")
html.colname <- paste("<td BGCOLOR= #66FF66>", colnames(mydata), "</td>", sep="", collapse="")
html.content <- paste(html.content, "<tr>", html.colname, "</tr>", sep="")
html.data <- NULL
for (i in 1:ncol(mydata))
{
tmp <- mydata[,i]
if (length(unique(tmp))>=5 && is.numeric(tmp))
{
order.index <- order(as.numeric(tmp))
# TODO: have more color choice?
quantile.index <- round(quantile(1:length(order.index), c(0.25,0.5,0.75)))
# q25, 50, 75, 100
q25.index <- c(1:quantile.index[1])
if (quantile.index[1]!=quantile.index[2]) q50.index <- c((quantile.index[1]+1):quantile.index[2])
if (quantile.index[2]!=quantile.index[3]) q75.index <- c((quantile.index[2]+1):quantile.index[3])
if (quantile.index[3] < length(order.index)) q100.index <- c((quantile.index[3]+1):(length(order.index)))
tmp[order.index[q25.index]] <- paste("<td BGCOLOR= #33FFFF>", tmp[order.index[q25.index]], "</td>", sep="")
tmp[order.index[q50.index]] <- paste("<td BGCOLOR= #FFFF99>", tmp[order.index[q50.index]], "</td>", sep="")
tmp[order.index[q75.index]] <- paste("<td BGCOLOR= #FFCC00>", tmp[order.index[q75.index]], "</td>", sep="")
tmp[order.index[q100.index]] <- paste("<td BGCOLOR= #FF6600>", tmp[order.index[q100.index]], "</td>", sep="")
}
else
{
if (length(unique(tmp)) >=3 && is.numeric(tmp))
{
#min
min.index <- which(tmp==min(tmp))
max.index <- which(tmp==max(tmp))
tmp[min.index] <- paste("<td BGCOLOR= #33FFFF>", tmp[min.index], "</td>", sep="")
tmp[max.index] <- paste("<td BGCOLOR= #FF6600>", tmp[max.index], "</td>", sep="")
tmp[-c(min.index, max.index)] <- paste("<td>", tmp[-c(min.index, max.index)], "</td>", sep="")
}
else
{
tmp <- paste("<td>", tmp, "</td>", sep="")
}
}
mydata[,i] <- tmp
}
for (i in 1:nrow(mydata))
{
html.data <- paste(mydata[i,], sep="", collapse="")
html.content <- paste(html.content, "<tr>", html.data, "</tr>", sep="")
}
html.content <- paste(html.content, "</table>", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
# Create file with file name from input and content from input
# - input: 1. the html filename you want to creat
# 2. the content as a string
# - output: a html file
writeLst <- function(filename, lstString)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
# generate data file
#browser()
html.start<- paste(html.start, "<title>lst file",
"</title></header><body>", sep=" ")
html.start <- paste(html.start, "<hr><h3><p class=\"subtitle\">lst file</p></h3>", sep=" ")
html.content <- paste(lstString, "<br>", sep="")
html.content <- paste(html.content, collapse="")
html.content <- paste("<p><pre>", html.content, "</pre></p>", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
writeLst.tab <- function(filename, lstString)
{
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", package="PKreport"),
"http://129.186.62.12/PKreport.css",
"\"/>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
# generate data file
html.start<- paste(html.start, "<title>lst file",
"</title></header><body>", sep=" ")
html.content <- "<table>"
for (i in 1:length(lstString))
{
tmp <- strsplit(lstString[i], " ")[[1]]
tmp.html <- paste(tmp, collapse="</td><td>")
html.content <- paste(html.content, "<tr><td>", tmp.html, "</td></tr>", sep="")
}
html.content <- paste(html.content, "</table>", sep="")
PK.html <- file(filename, "w") # open an output file connection
html.all <- paste(html.start, html.content, html.end, sep="\n")
writeLines(html.all, con = PK.html, sep = "\n")
close(PK.html)
}
PKoutput <- function(nonmemObj=NULL, table.Rowv=FALSE, table.Colv=FALSE)
{
general.list <- .pkplot$getGlobalConfig()
# web browser compatibility
html.start <- "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\"
\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">"
html.start <- paste(html.start, "<html><header><link rel=\"stylesheet\"
type=\"text/css\" href=\"",
#system.file("doc", "PKreport.css", package="PKreport"),
"http://129.186.62.12/PKreport.css",
#"PKreport.css",
"\"/>", sep="")
html.index <- paste(html.start, "<title>PKreport</title></header><body>", sep="")
## add symbol image
html.index <- paste(html.index, "<h1><p class=\"title\">PKreport</p></h1>", sep="")
## general output
if ((!is.null(nonmemObj)) && class(nonmemObj) == "nonmem")
{
# start table
html.index <- paste(html.index,
"<h3><p class=\"subtitle\">NONMEM results</p></h3><table class=\"center\" border=0>",
sep="")
# lst file
if (length(nonmemObj@file.lst) != 0)
{
writeLst("lst.html", nonmemObj@file.lst)
html.index <- paste(html.index, "<tr><td><a href=lst.html>lst file</a></td></tr>", sep="")
}
# tab file, match that in "nonmem" class
if (nrow(nonmemObj@tabdata) != 0)
{
order.data <- nonmemObj@tabdata
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("tab.html", "tab file", order.data)
html.index <- paste(html.index, "<tr><td><a href=tab.html>Tab file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.cov$data) != 0)
{
order.data <- nonmemObj@file.cov$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("cov.html", "cov file",order.data)
html.index <- paste(html.index, "<tr><td><a href=cov.html>Cov file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.cor$data) != 0)
{
order.data <- nonmemObj@file.cor$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("cor.html", "cor file",order.data)
html.index <- paste(html.index, "<tr><td><a href=cor.html>Cor file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.coi$data) != 0)
{
order.data <- nonmemObj@file.coi$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("coi.html", "coi file",order.data)
html.index <- paste(html.index, "<tr><td><a href=coi.html>Coi file</a></td></tr>", sep="")
}
if (nrow(nonmemObj@file.phi$data) != 0)
{
order.data <- nonmemObj@file.phi$data
if (table.Colv || table.Rowv)
{
tmp.data <- order.data[,sapply(order.data, is.numeric)]
tmp.heat <- heatmap(as.matrix(tmp.data))
if (table.Rowv) order.data <- order.data[rev(tmp.heat$rowInd),]
if (table.Colv) order.data <- order.data[, tmp.heat$colInd]
}
writeTable("phi.html", "phi file",order.data)
html.index <- paste(html.index, "<tr><td><a href=phi.html>phi file</a></td></tr>", sep="")
}
}
#########################
## add separator
#########################
html.index <- paste(html.index, "</table><hr><h3><p class=\"subtitle\">Diagnostics</p></h3><table class=\"center\" border=0>", sep="")
## univariate figures
if (file.exists(general.list$univar.dir))
{
writeHTML(general.list$univar.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKunivar.html>Univariate Figures</a></td></tr>", sep="")
}
## bivariate figures
if (file.exists(general.list$bivar.dir))
{
writeHTML(general.list$bivar.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKbivar.html>Bivariate Figures</a></td></tr>", sep="")
}
## bivariate figures
if (file.exists(general.list$ind.dir))
{
writeHTML(general.list$ind.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKind.html>Individual Figures</a></td></tr>", sep="")
}
## gof figures
if (file.exists(general.list$gof.dir))
{
writeHTML(general.list$gof.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKgof.html>Figures for Goodness of Fit</a></td></tr>", sep="")
}
if (file.exists(general.list$struct.dir))
{
writeHTML(general.list$struct.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKstruct.html>Figures for Structural Model Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$resid.dir))
{
writeHTML(general.list$resid.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKresid.html>Figures for Residual Model Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$para.dir))
{
writeHTML(general.list$para.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKpara.html>Figures for Parameters Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$cov.dir))
{
writeHTML(general.list$cov.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKcov.html>Figures for Covariate Model Dagnostics</a></td></tr>", sep="")
}
if (file.exists(general.list$eta.dir))
{
writeHTML(general.list$eta.dir,general.list$save.format)
html.index <- paste(html.index, "<tr><td><a href=PKeta.html>Figures for Random Effects Dagnostics</a></td></tr>", sep="")
}
if (file.exists("PKcode.txt"))
{
html.index <- paste(html.index, "<tr><td><a href=PKcode.txt>R Code for Figures</a></td></tr>", sep="")
}
# end table
html.index <- paste(html.index, "</table>", sep="")
html.end <- paste("<p></p><p></p><hr><p align=\"right\" class=\"bottomFont\">PKreport", packageDescription("PKreport")$Version,
date(), "</p></body></html>", sep=" ")
html.index <- paste(html.index, html.end, sep="")
PK.html <- file("PKindex.html", "w") # open an output file connection
writeLines(html.index, con = PK.html, sep = "\n")
close(PK.html)
}
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