simmons_genome_diversity_oct_2016.Rnw

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  13 \usepackage{booktabs}
  14 % \usepackage{multirow}
  15 \usepackage{acronym}
  16 \usepackage{qrcode}
  17 \usepackage[backend=biber,natbib=true,hyperref=true,style=nature]{biblatex}
  18 \addbibresource{references.bib}
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  52
  53 \title[Ancestry]{Simmons Genome Diversity}
  54 \author[Don Armstrong]{Don L. Armstrong}
  55 \institute[IGB]{Institute for Genomic Biology, Computing Genomes
  56   for Reproductive Health, University of Illinois, Urbana-Champaign}
  57
  58 \begin{document}
  59
  60 <<load.libraries,echo=FALSE,results="hide",warning=FALSE,message=FALSE,error=FALSE,cache=FALSE>>=
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  63 options(device = function(file, width = 8, height = 7, ...) {
  64   cairo_pdf(tempfile(), width = width, height = height, ...)
  65 })
  66 options(digits=2)
  67 library("data.table")
  68 library("ggplot2")
  69 library("reshape2")
  70 library("grid")
  71 library("xtable")
  72
  73 @
  74
  75 \IfFileExists{figures/relevant_xkcd.png}{\frame[plain]{\centering \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{figures/relevant_xkcd.png}
  76
  77     \url{https://xkcd.com/1706/}}}
  78
  79 \frame[plain]{\titlepage
  80   \begin{center}
  81     Code and slides are here:
  82
  83     \qrcode[padding]{http://dla2.us/p/genomdev2016}
  84
  85     \url{http://dla2.us/p/genomdev2016}
  86    \end{center}
  87 }
  88
  89
  90 \frame[plain]{
  91    \begin{center}
  92      \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/title.png}
  93    \end{center}
  94 }
  95
  96 \begin{frame}{Relatedness of Populations}
  97   \begin{columns}
  98     \column{0.7\textwidth}
  99     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_1.png}
 100     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_2.png}
 101     \column{0.3\textwidth}
 102     \begin{itemize}
 103     \item Neighbor joining tree based on pairwise divergence per nucleotide
 104     \item Deepest splits are in African populations
 105     \end{itemize}
 106   \end{columns}
 107 \end{frame}
 108
 109 \begin{frame}{PCA and Relatedness}
 110   \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig_ed4.png}
 111 \end{frame}
 112
 113 \begin{frame}
 114   \begin{center}
 115     \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1b.png}
 116   \end{center}
 117 \end{frame}
 118
 119 \begin{frame}
 120   \begin{center}
 121     \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1c.png}
 122   \end{center}
 123 \end{frame}
 124
 125 \begin{frame}
 126   \begin{center}
 127     \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1d.png}
 128   \end{center}
 129 \end{frame}
 130
 131
 132 \begin{frame}
 133   \begin{center}
 134     \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig_ed1.png}
 135   \end{center}
 136 \end{frame}
 137
 138 \begin{frame}
 139   \begin{center}
 140     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2a.png}
 141     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2b.png}
 142   \end{center}
 143 \end{frame}
 144
 145 \begin{frame}
 146   \begin{center}
 147     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2c.png}
 148     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2d.png}
 149   \end{center}
 150 \end{frame}
 151
 152 \begin{frame}
 153   \begin{center}
 154     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2e.png}
 155     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2f.png}
 156   \end{center}
 157 \end{frame}
 158
 159
 160 \section*{References}
 161
 162 \begin{frame}[plain]{References}
 163   \begin{center}
 164     \mbox{}\vspace{-\baselineskip}
 165     \printbibliography[heading=none]
 166   \end{center}
 167 \end{frame}
 168
 169 \end{document}