add start of presentation and figure makefile

diff --git a/diamond_presentation_2015.Rnw b/diamond_presentation_2015.Rnw
new file mode 100644 (file)
index 0000000..2ed4cf2
--- /dev/null
+++ b/diamond_presentation_2015.Rnw
@@ -0,0 +1,122 @@
+\documentclass[ignorenonframetext]{beamer}
+\usepackage{fontspec}
+\setmainfont{FreeSerif}
+\setsansfont{FreeSans}
+\setmonofont{FreeMono}
+\usepackage{url}
+\usepackage{fancyhdr}
+\usepackage{graphicx}
+\usepackage[bf]{caption}
+\usepackage{rotating}
+\usepackage{wrapfig}
+\usepackage{fancybox}
+\usepackage{booktabs}
+% \usepackage{multirow}
+\usepackage{acronym}
+\usepackage{qrcode}
+\usepackage[backend=biber,natbib=true,hyperref=true,style=nature]{biblatex}
+\addbibresource{references.bib}
+% \usepackage[nomargin,inline,draft]{fixme}
+% \newcommand{\DLA}[1]{\textcolor{red}{\fxnote{DLA: #1}}}
+% \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref}
+\usepackage{texshade}
+\usepackage{tikz}
+\usepackage{nameref}
+\usepackage{zref-xr,zref-user}
+\renewcommand*{\bibfont}{\tiny}
+
+% The textpos package is necessary to position textblocks at arbitary 
+% places on the page.  Use showboxes option to show outlines of textboxes.
+% \usepackage[absolute]{textpos}
+\usepackage[absolute,showboxes]{textpos}
+
+\usepackage{multirow}
+\usepackage{array}
+
+\mode<presentation>{ 
+  \usetheme{CambridgeUS}
+  % http://identitystandards.illinois.edu/graphicstandardsmanual/generalguidelines/colors.html
+  \definecolor{ilboldblue}{HTML}{002058}
+  \definecolor{ilboldorange}{HTML}{E87722}
+  \definecolor{ilblue}{HTML}{606EB2}
+  \definecolor{ilorange}{HTML}{D45D00}
+  \setbeamercolor{alerted text}{fg=ilboldorange}
+  \setbeamercolor*{palette primary}{fg=ilblue,bg=ilorange}
+  \setbeamercolor*{palette secondary}{fg=ilblue!20!white,bg=ilorange}
+  \setbeamercolor*{palette tertiary}{bg=ilblue,fg=ilorange}
+  \setbeamercolor*{palette quaternary}{fg=ilblue,bg=ilorange}
+  
+  \setbeamercolor*{sidebar}{fg=ilorange,bg=ilboldblue}
+  
+  \setbeamercolor*{palette sidebar primary}{fg=ilblue!10!white,bg=ilorange}
+  \setbeamercolor*{palette sidebar secondary}{fg=ilorange}
+  \setbeamercolor*{palette sidebar tertiary}{fg=ilblue}
+  \setbeamercolor*{palette sidebar quaternary}{fg=ilorange}
+  
+  % \setbeamercolor*{titlelike}{parent=palette primary}
+  \setbeamercolor{titlelike}{parent=palette primary,fg=ilboldblue,bg=ilorange}
+  \setbeamercolor{frametitle}{fg=ilboldorange,bg=ilblue!80!white}
+  \setbeamercolor{frametitle right}{fg=ilboldblue,bg=ilorange}
+  
+  \setbeamercolor*{separation line}{}
+  \setbeamercolor*{fine separation line}{}
+  \setbeamercovered{transparent}  
+  \logo{\begin{tikzpicture}% Pale figure
+      {\node[opacity=0.8]{\IfFileExists{figures/igb_wordmark.pdf}{\includegraphics[width=2cm,height=1cm,keepaspectratio]{figures/igb_wordmark}}{}%
+        };}%
+    \end{tikzpicture}}
+}
+
+\title[DIAMOND]{DIAMOND: Fast protein alignment}
+\author[Don Armstrong]{Don L. Armstrong}
+\institute[IGB]{Institute for Genomic Biology, Computing Genomes 
+  for Reproductive Health, University of Illinois, Urbana-Champaign}
+
+\begin{document}
+
+<<load.libraries,echo=FALSE,results="hide",warning=FALSE,message=FALSE,error=FALSE,cache=FALSE>>=
+opts_chunk$set(dev="cairo_pdf",out.width="\\textwidth",out.height="0.8\\textheight",out.extra="keepaspectratio")
+#opts_chunk$set(cache=TRUE, autodep=TRUE)
+options(device = function(file, width = 8, height = 7, ...) {
+  cairo_pdf(tempfile(), width = width, height = height, ...)
+})
+options(digits=2)
+library("data.table")
+library("ggplot2")
+library("reshape2")
+library("grid")
+library("xtable")
+
+@ 
+
+\IfFileExists{figures/relevant_xkcd.png}{\frame[plain]{\centering \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{figures/relevant_xkcd.png}
+
+    \url{https://xkcd.com/1513/}}}
+
+\frame[plain]{\titlepage}
+
+
+
+\section{The Problem}
+
+\section{The Previous Contenders}
+
+\section{Diamond Methodology}
+
+\section{Comparison}
+
+\subsection{Speed}
+
+\subsection{Accuracy}
+
+
+\section*{References}
+
+\begin{frame}[plain]{References}
+  \begin{center}
+    \mbox{}\vspace{-\baselineskip}
+    \printbibliography[heading=none]
+  \end{center}
+\end{frame}
+
+\end{document}

diff --git a/figures/Makefile b/figures/Makefile
new file mode 100644 (file)
index 0000000..516d6ce
--- /dev/null
+++ b/figures/Makefile
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+all: uofi_mark.pdf igb_wordmark.pdf
+
+igb_wordmarks.zip: 
+       wget -O $@ "http://www.igb.illinois.edu/sites/default/files/upload/Wordmarks-Eps.zip"
+
+igb_wordmark.pdf: igb_wordmarks.zip
+       unzip igb_wordmarks.zip Wordmark-black-tag-outlines.eps
+       epstopdf --outfile=$@ Wordmark-black-tag-outlines.eps
+       rm -f Wordmark-black-tag-outlines.eps
+
+uofi_mark.zip: 
+       wget -O $@ "http://identitystandards.illinois.edu/assets/logos/uclogo_1867_horz_bold.zip"
+
+uofi_mark.pdf: uofi_mark.zip
+       unzip uofi_mark.zip uclogo_1867_horz_bold/pc/uclogo_1867_horz_bold.eps
+       epstopdf --outfile=$@ uclogo_1867_horz_bold/pc/uclogo_1867_horz_bold.eps
+       rm -rf uclogo_1867_horz_bold
+
+relevant_xkcd.png:
+       wget -O $@ "http://imgs.xkcd.com/comics/code_quality.png"