From 7f48095d35cde84d0d1ff168bd5d241a798563b0 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Wed, 19 Oct 2016 12:47:44 -0500 Subject: [PATCH] add start of genome diversity paper --- figures/Makefile | 22 ++++ genome_diversity_paper/Makefile | 27 ++++ simmons_genome_diversity_oct_2016.Rnw | 169 ++++++++++++++++++++++++++ 3 files changed, 218 insertions(+) create mode 100644 figures/Makefile create mode 100644 genome_diversity_paper/Makefile create mode 100644 simmons_genome_diversity_oct_2016.Rnw diff --git a/figures/Makefile b/figures/Makefile new file mode 100644 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 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 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{ + \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} + +<>= +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} -- 2.39.2