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\documentclass{combine}
\usepackage{combine}
\usepackage{geometry}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{pdflscape}
\usepackage{fancyhdr}
\usepackage[iso]{isodateo}
\usepackage{Sweave}
\geometry{tmargin=2cm,bmargin=2.5cm,lmargin=2cm,rmargin=2cm}
\pagestyle{fancy}
\headheight 25pt
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
\begin{document}
\begin{titlepage}
\begin{center}
% Upper part of the page
\HRule \\[0.7cm]
\textsc{\huge EXAMPLE Biomarker Study} \\[1.5cm]
\textsc{\huge $A\beta_{1-42}$, $t-tau$ and $p-tau_{181P}$} \\[0.5cm]
\HRule \\[3.5cm]
{ \LARGE \bfseries Part 1. Project QC summary\\[0.3cm]
Part 2. Individual plate reports}\\[1.0cm]
\Large Created in ``R'' and \LaTeX{}
\vfill
% Date
{\large \today}\\[1.0cm]
% Authors - bottom of the page
\begin{minipage}{0.4\textwidth}
\begin{flushleft} \large
\emph{Created by:}\\
Michal J. \textsc{Figurski}, PhD.
\end{flushleft}
\end{minipage}
\begin{minipage}{0.4\textwidth}
\begin{flushright} \large
\emph{Reviewed by:} \\
Leslie M. \textsc{Shaw}, PhD.
\end{flushright}
\end{minipage}
\end{center}
\end{titlepage}
\newpage
\mbox{}
\vfill
\begin{center}
\section*{\huge Part 1. Project QC summary}
\end{center}
\vfill
\newpage
\lhead{General QC Summary}
\rhead{Project: \textsc{\Sexpr{immunoassay.environment$project.options$template} }}
<<results=tex, echo=FALSE>>=
.a = immunoassay.environment$results
.a$Type[.a$Type=="Retest"] = "Sample"
.b = project.means(.a)
.b$Kit = factor(.b$Kit)
.b = .b[order(.b$Kit, .b$ID, .b$Type, .b$SPL),]
.bb = list(c("St7"),c("St6","St5"),c("St4","St3"),c("St2","St1"),c("pool48","pool52"))
# Project-level plots:
for (i2 in 1:length(.bb)) {
CairoPDF(file=paste(immunoassay.environment$path, "/Tex/pdf/psum-", i2, sep=""), width=14, height=8)
par(mfrow=c(1,2))
.bc = c(1, length(unique(.b$ID)))
if (i2 == 1) .bc = c(1,15,17,20,24,35,length(unique(.b$ID)))
if (i2 %in% 2:4) .bc = c(1,17,20,24,35,length(unique(.b$ID)))
project.qcplot(.b, samples=.bb[[i2]], breaks=.bc)
dev.off()
cat("\\vfill\n")
cat("\\begin{center}\n", sep="")
cat(" \\includegraphics[width=1.01\\textwidth]{\"", "pdf/psum-",i2, "\"}\n", sep="")
cat("\\end{center}\n\n", sep="")
cat("\\vfill\n")
}
@
\newpage
\lhead{ }
\rhead{ }
\mbox{}
\vfill
\begin{center}
\section*{\huge Part 2. Individual plate reports}
\end{center}
\vfill
\newpage
\lhead{Data interpretation report}
\rhead{Acquisition Time: \Sexpr{attr(immunoassay.environment$l.run,"Date")} }
\rfoot{Page: \thepage}
\cfoot{Report Date: \today}
\setcounter{secnumdepth}{-1 }
\pagestyle{combine}
\begin{papers}
<<results=tex, echo=FALSE>>=
for (i1 in immunoassay.environment$files) {
i2 = substr(i1,0, nchar(i1)-4)
cat(paste("\\import{\"",i2,"\"} \n\n", sep=""))
}
# Clean-up
rm(.a,.b,.bb,.bc,i1,i2)
@
\end{papers}
\end{document}
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