add start of genome diversity paper

diff --git a/figures/Makefile b/figures/Makefile
new file mode 100644 (file)
index 0000000..ae6f912
--- /dev/null
+++ b/figures/Makefile
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+all: uofi_mark.pdf igb_wordmark.pdf spalax.jpg reduced_alphabet.png
+
+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/genetic_testing.png"

diff --git a/genome_diversity_paper/Makefile b/genome_diversity_paper/Makefile
new file mode 100644 (file)
index 0000000..6affdce
--- /dev/null
+++ b/genome_diversity_paper/Makefile
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+
+all: paper_figures supplemental_images supp_data_1.xlsx supp_data_2.xlsx
+
+supplemental_images: supplemental_info.pdf
+       pdfimages -j -png $< supplemental && touch $@
+
+paper.pdf:
+       wget -O $@ "http://www.nature.com/nature/journal/v538/n7624/pdf/nature18964.pdf"
+
+supplemental_info.pdf:
+       wget -O $@ "http://www.nature.com/nature/journal/v538/n7624/extref/nature18964-s1.pdf"
+
+supp_data_1.xlsx:
+       wget -O $@ "http://www.nature.com/nature/journal/v538/n7624/extref/nature18964-s2.xlsx"
+
+supp_data_2.xlsx:
+       wget -O $@ "http://www.nature.com/nature/journal/v538/n7624/extref/nature18964-s3.xlsx"
+
+paper_figures: extract_figures.pl paper.pdf
+       perl $<;
+       touch paper_figures;
+
+.PHONY: clean
+
+clean:
+       rm -f *.png *.pdf *.xlsx

diff --git a/simmons_genome_diversity_oct_2016.Rnw b/simmons_genome_diversity_oct_2016.Rnw
new file mode 100644 (file)
index 0000000..04814b4
--- /dev/null
+++ b/simmons_genome_diversity_oct_2016.Rnw
@@ -0,0 +1,169 @@
+\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,overlay]{textpos}
+\usepackage{mathtools,cancel}
+
+\renewcommand{\CancelColor}{\color{red}} %change cancel color to red
+
+\usepackage{multirow}
+\usepackage{array}
+
+\mode<presentation>{ 
+  \usetheme{CambridgeUS}
+  \usecolortheme{crane}
+  % http://identitystandards.illinois.edu/graphicstandardsmanual/generalguidelines/colors.html
+  \definecolor{ilboldblue}{HTML}{002058}
+  \definecolor{ilboldorange}{HTML}{E87722}
+  \definecolor{ilblue}{HTML}{606EB2}
+  \definecolor{ilorange}{HTML}{D45D00}
+  \logo{\begin{tikzpicture}% Pale figure
+      {\node[opacity=0.6]{\IfFileExists{figures/uofi_mark.pdf}{\includegraphics[width=2cm,height=1cm,keepaspectratio]{figures/uofi_mark}}{}%
+        };}%
+    \end{tikzpicture}}
+}
+
+\title[Ancestry]{Simmons Genome Diversity}
+\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/1706/}}}
+
+\frame[plain]{\titlepage
+  \begin{center}
+    Code and slides are here: 
+    
+    \qrcode[padding]{http://dla2.us/p/genomdev2016}
+    
+    \url{http://dla2.us/p/genomdev2016}
+   \end{center}
+}
+ 
+
+\frame[plain]{
+   \begin{center}
+     \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/title.png}
+   \end{center}
+}
+
+\begin{frame}{Relatedness of Populations}
+  \begin{columns}
+    \column{0.7\textwidth}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_1.png}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_2.png}
+    \column{0.3\textwidth}
+    \begin{itemize}
+    \item Neighbor joining tree based on pairwise divergence per nucleotide
+    \item Deepest splits are in African populations
+    \end{itemize}
+  \end{columns}
+\end{frame}
+
+\begin{frame}{PCA and Relatedness}
+  \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig_ed4.png}
+\end{frame}
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1b.png}
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1c.png}
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1d.png}
+  \end{center}
+\end{frame}
+
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig_ed1.png}
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2a.png}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2b.png}
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2c.png}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2d.png}
+  \end{center}
+\end{frame}
+
+\begin{frame}
+  \begin{center}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2e.png}
+    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2f.png}
+  \end{center}
+\end{frame}
+
+
+\section*{References}
+
+\begin{frame}[plain]{References}
+  \begin{center}
+    \mbox{}\vspace{-\baselineskip}
+    \printbibliography[heading=none]
+  \end{center}
+\end{frame}
+
+\end{document}