From d26e7161b480026053610eb7143e1d02cbc37ab6 Mon Sep 17 00:00:00 2001 From: "Philipp Homan yoga ubuntu 17.10" Date: Thu, 5 Apr 2018 16:09:37 +0200 Subject: [PATCH] Cleaned up again --- src/#org-mode-poster_poster.org# | 373 ------------------------------- src/emacs.svg | 286 ------------------------ src/org-mode-poster_ms.tex~ | 24 -- 3 files changed, 683 deletions(-) delete mode 100644 src/#org-mode-poster_poster.org# delete mode 100644 src/emacs.svg delete mode 100644 src/org-mode-poster_ms.tex~ diff --git a/src/#org-mode-poster_poster.org# b/src/#org-mode-poster_poster.org# deleted file mode 100644 index 8a8c27d..0000000 --- a/src/#org-mode-poster_poster.org# +++ /dev/null @@ -1,373 +0,0 @@ -#+startup: beamer -#+TITLE: Using org-mode for scientific posters -* Preamble :ignore: -** General comments :ignore: -# ---------------------------------------------------------------------- -# - Turn on synonyms by starting synosaurus-mode -# - Look up words using C-c sr -# - Turn on dictionary by starting flyspell-mode -# - Count words by section using org-wc-display -# ---------------------------------------------------------------------- -** Specific comments for this manuscript :ignore: -# ---------------------------------------------------------------------- -# This is a comment -# ---------------------------------------------------------------------- -** org specific settings :ignore: -# ---------------------------------------------------------------------- -#+OPTIONS: email:nil toc:nil num:nil author:nil date:t tex:t title:nil -#+STARTUP: align fold -#+SEQ_TODO: TODO(t) | DONE(d) -#+TAGS: figure(f) check(c) noexport(n) ignore(i) -#+LANGUAGE: en -#+EXCLUDE_TAGS: noexport TODO -#+DATE: {{{time(%Y-%m-%d %H:%M)}}} -# ---------------------------------------------------------------------- -** Latex header :ignore: -# ---------------------------------------------------------------------- -#+LATEX_CLASS: mybeamerposter -#+LATEX_HEADER: \setlength{\paperwidth}{36in} -#+LATEX_HEADER: \setlength{\paperheight}{48in} -#+LATEX_HEADER: \setlength{\textwidth}{0.98\paperwidth} -#+LATEX_HEADER: \setlength{\textheight}{0.98\paperheight} -#+LATEX_HEADER: \graphicspath{{../output/figures/}{../lib/}} -#+LATEX_HEADER: \usepackage[export]{adjustbox} -#+LATEX_HEADER: \usepackage{graphicx,caption} -#+LATEX_HEADER: \usepackage{minted} -#+LATEX_HEADER: \usepackage{eurosym} -#+LATEX_HEADER: \usepackage{listings} -#+LATEX_HEADER: \usepackage{textcomp} -#+LATEX_HEADER: \usepackage{bibentry} -#+LATEX_HEADER: \newcommand\sumin{\sum_{i=1}^{n}} -#+LATEX_HEADER: \newcommand{\Xoi}[1]{#1(i)} -#+LATEX_HEADER: \newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}} -#+LATEX_HEADER: \newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)} -#+LATEX_HEADER: \date{} -# ---------------------------------------------------------------------- -** Latex macros :ignore: -# ---------------------------------------------------------------------- -#+LATEX_HEADER: \newcommand{\auth}{Philipp Homan, MD, PhD} -#+LATEX_HEADER: \newcommand{\authemail}{phoman1@northwell.edu} -#+LATEX_HEADER: \newcommand{\authtwitter}{@philipphoman} -#+LATEX_HEADER: \newcommand{\authgithub}{github.com/philipphoman} -# ---------------------------------------------------------------------- -** Authors and affiliations :ignore: -# ---------------------------------------------------------------------- -#+LATEX_HEADER: \author{ -#+LATEX_HEADER: Philipp Homan$^{1}$ -#+LATEX_HEADER: \\ -#+LATEX_HEADER: \normalsize{$^{1}$Department of Psychiatry,} -#+LATEX_HEADER: \normalsize{The Donald and Barbara Zucker} -#+LATEX_HEADER: \normalsize{School of Medicine at Northwell/Hofstra,} -#+LATEX_HEADER: \normalsize{Hempstead, NY} -#+LATEX_HEADER: } -# ---------------------------------------------------------------------- -** Buffer-wide source code blocks :ignore: -# ---------------------------------------------------------------------- -# Set elisp variables need for nice formatting We want no new lines in -# inline results and a paragraph size of 80 characters Important: this -# has to be evaluated witch C-c C-c in order to work in the current -# buffer -#+BEGIN_SRC emacs-lisp :exports none :results silent - - ; Nicer formatting for code - (setq org-latex-listings t) - (setq org-latex-listings 'minted) - '(org-export-latex-listings-langs - (quote ((emacs-lisp "Lisp") - (lisp "Lisp") - (clojure "Lisp") - (c "C") - (cc "C++") - (fortran "fortran") - (perl "Perl") - (cperl "Perl") - (python "Python") - (ruby "Ruby") - (html "HTML") - (xml "XML") - (tex "TeX") - (latex "TeX") - (shell-script "bash") - (gnuplot "Gnuplot") - (ocaml "Caml") - (caml "Caml") - (sql "SQL") - (sqlite "sql") - (R-mode "R")))) - (setq org-latex-minted-options - '(("linenos=true") ("bgcolor=lightgray"))) - ; set timestamp format - ;(setq org-export-date-timestamp-format "%FT%T%z") - (require 'org-wc) - (flyspell-mode t) - ;(evil-declare-change-repeat 'company-complete) - (setq synosaurus-choose-method 'popup) - (synosaurus-mode t) - (auto-complete-mode t) - ;(ac-config-default) - ;(add-to-list 'ac-modes 'org-mode) - (linum-mode t) - (whitespace-mode t) - (setq org-babel-inline-result-wrap "%s") - (setq org-export-with-broken-links "mark") - (setq fill-column 72) - (setq whitespace-line-column 72) - ;(setq org-latex-caption-above '(table image)) - (setq org-latex-caption-above nil) - (org-toggle-link-display) - ; don't remove logfiles at export - (setq org-latex-remove-logfiles nil) - - ; Keybindings - ; (global-set-key (kbd " c") "#+CAPTION: ") - (defun setfillcolumn72 () - (interactive) - (setq fill-column 72) - ) - - (defun setfillcolumn42 () - (interactive) - (setq fill-column 42) - ) - (define-key org-mode-map (kbd "C-c c #") "#+CAPTION: ") - (define-key org-mode-map (kbd "C-c l #") "#+LATEX_HEADER: ") - (define-key org-mode-map (kbd "C-c f c 4 2") 'setfillcolumn42) - (define-key org-mode-map (kbd "C-c f c 7 2") 'setfillcolumn72) - - (setq org-odt-category-map-alist - '(("__Figure__" "*Figure*" "value" "Figure" org-odt--enumerable-image-p))) - - - ; let ess not ask for starting directory - (setq ess-ask-for-ess-directory nil) - - ;(setq org-latex-pdf-process '("latexmk -pdflatex='xelatex - ;-output-directory=../output/tex/ -interaction nonstopmode' -pdf - ;-bibtex -f %f")) - (setq org-latex-logfiles-extensions - (quote("bcf" "blg" "fdb_latexmk" "fls" - "figlist" "idx" "log" "nav" "out" "ptc" - "run.xml" "snm" "toc" "vrb" "xdv"))) - - ; deactivate link resolving - (setq org-activate-links nil) - - -#+END_SRC -# -# -# -# ---------------------------------------------------------------------- -** End preamble :ignore: -# ---------------------------------------------------------------------- - -* The poster -:PROPERTIES: -:BEGIN: -:BEAMER_env: fullframe -:END: -** Code :ignore: -# Babel code can go here to populate the poster with dynamic output - -** Left column :BMCOL: -:PROPERTIES: -:BEAMER_col: 0.45 -:BEAMER_opt: [t] -:END: -*** Background :B_block: -:PROPERTIES: -:BEAMER_env: block -:END: -- Here we show how org-mode (version src_elisp{org-version} - {{{results(9.1.7)}}}) and emacs (version src_elisp{emacs-version} - {{{results(25.2.2)}}}) can be used to make decent looking scientific - posters -- With org-mode we can populate the poster with code, graphs and numbers - from inline code in languages such as R, python, Matlab and even shell - scripting -- For example, this poster was created on {{{time(%Y-%m-%d %H:%M)}}} on - src_bash{lsb_release -sd} {{{results(Ubuntu 17.10)}}}. -- Inline code could look like this (which will produce a graph; - Fig. [[figcode1]]): - -**** Block -:PROPERTIES: -:BEAMER_col: 0.68 -:BEAMER_opt: [T] -:END: - -#+NAME: code1 -#+BEGIN_SRC R :file 3.png :session :exports both :results graphics -set.seed(20180402) -x1 <- rnorm(100, 0, 1) -x2 <- rnorm(100, 0.5, 1) -hist(x1, col="red") -hist(x2, col="blue", add=TRUE) -#+END_SRC - -#+NAME: figcode1 -#+CAPTION: This is the output. -#+RESULTS: code1 -[[file:3.png]] - -*** Inline code and tables :B_block: -:PROPERTIES: -:BEAMER_env: block -:END: -- In addition to inline code, we can also produce tables -- Tables are very powerful in org-mode, they even include spreadsheet - capabilities -- Some code to process the first vector from above to make a table out - of its summary could look like this, which would result in a little - table (Table [[tabcode2]]) : - -**** Block -:PROPERTIES: -:BEAMER_col: 0.78 -:BEAMER_opt: [T] -:END: - -#+NAME: code2 -#+BEGIN_SRC R :session :exports both :results value :colnames yes :cache yes -library(broom) -library(dplyr) -t1 <- tidy(round(summary(x1), 2)) -t2 <- tidy(round(summary(x2), 2)) - -# This will export as a table -rbind(t1, t2) %>% -mutate(name=c("x1", "x2")) -#+END_SRC - -\vspace{2cm} - -#+CAPTION: A table summarizing the two distributions. -#+NAME: tabcode2 -#+RESULTS[9d0ec7348265a5cb6de39440ff06a8dbb8e5ecf1]: code2 -|---------+-------+--------+------+------+---------+------| -| minimum | q1 | median | mean | q3 | maximum | name | -|---------+-------+--------+------+------+---------+------| -| -2.29 | -0.49 | 0.11 | 0.14 | 0.8 | 2.47 | x1 | -| -2.17 | -0.45 | 0.07 | 0.13 | 0.85 | 2.23 | x2 | -|---------+-------+--------+------+------+---------+------| - -** Right column :BMCOL: -:PROPERTIES: -:BEAMER_col: 0.45 -:BEAMER_opt: [t] -:END: -*** Graphics :B_block: -:PROPERTIES: -:BEAMER_env: block -:END: - -- We can use shell scripting to grab an image with curl from the - internet (Fig. [[figcode3]]): - -**** Block -:PROPERTIES: -:BEAMER_col: 0.78 -:BEAMER_opt: [T] -:END: - -\footnotesize -#+NAME: code3 -#+BEGIN_SRC bash :exports both :file emacs.png -# Download emacs icon from gnu.org -curl -0 https://www.gnu.org/software/emacs/images/emacs.png -#+END_SRC -\normalsize - -\vspace{2cm} - -#+ATTR_LATEX: :width 0.2\textwidth :options page=9 -#+NAME: figcode3 -#+CAPTION: This is the downloaded image. -#+RESULTS: code3 -[[file:emacs.png]] - -*** Math :B_block: -:PROPERTIES: -:BEAMER_env: block -:END: - -- We can easily include math -- For example, let's describe how to compute the distance between the - two simulated distributions $x1$ and $x2$ from before: - -**** Block -:PROPERTIES: -:BEAMER_col: 0.78 -:BEAMER_opt: [T] -:END: - -The Kullback-Leibler (KL) divergence measures the difference between two -probability distributions (i.e., the loss of information when one -distribution is used to approximate another). The KL divergence is thus -defined as - -\begin{align} -\label{eq:KL} -\DKLPQ{P}{Q}{\|} = \sumin \Xoi{P} \log \frakPQ{P}{Q} -\end{align} - -with $P$ and $Q$ being two probability distribution functions and $n$ -the number of sample points. Since $\DKLPQ{P}{Q}{\|}$ is not equal to -$\DKLPQ{Q}{P}{\|}$, a symmetric variation of the KL divergence can be -derived as follows: - -\begin{align} -\label{eq:KL2} -\DKLPQ{P}{Q}{,} = \sumin \Big(\Xoi{P} \log \frakPQ{P}{Q} + \Xoi{Q} \log \frakPQ{Q}{P} \Big). -\end{align} - -*** Columns :B_block: -:PROPERTIES: -:BEAMER_env: block -:END: - -**** Left -:PROPERTIES: -:BEAMER_col: 0.48 -:BEAMER_opt: [T] -:END: - -#+NAME: codeleft -#+BEGIN_SRC R :file 4l.png :session :exports results :results graphics -d1 <- density(x1) -plot(d1, col="red", lwd=3) -#+END_SRC - - -\captionsetup{justification=justified,width=.85\linewidth} -#+NAME: figcodeleft -#+CAPTION: This is the left figure of a two-column block, showing -#+CAPTION: the density of $x1$. -#+RESULTS: codeleft -[[file:4l.png]] - -**** Right -:PROPERTIES: -:BEAMER_col: 0.48 -:BEAMER_opt: [T] -:END: - -#+NAME: coderight -#+BEGIN_SRC R :file 4r.png :session :exports results :results graphics -d2 <- density(x2) -plot(d2, col="blue", lwd=3) -#+END_SRC - -\captionsetup{justification=justified,width=.85\linewidth} -#+NAME: figcoderight -#+CAPTION: This is the right figure. It shows the density of $x2$. -#+RESULTS: coderight -[[file:4r.png]] - -*** Conclusions :B_block: -:PROPERTIES: -:BEAMER_env: block -:END: -- This little example is meant to show how versatile org-mode is -- Scientific posters can be produced with a simple text editor - diff --git a/src/emacs.svg b/src/emacs.svg deleted file mode 100644 index 632d53e..0000000 --- a/src/emacs.svg +++ /dev/null @@ -1,286 +0,0 @@ - -image/svg+xml diff --git a/src/org-mode-poster_ms.tex~ b/src/org-mode-poster_ms.tex~ deleted file mode 100644 index bb6aeb3..0000000 --- a/src/org-mode-poster_ms.tex~ +++ /dev/null @@ -1,24 +0,0 @@ -% Created 2018-04-03 Tue 04:57 -% Intended LaTeX compiler: pdflatex -\documentclass[11pt]{article} -\usepackage[utf8]{inputenc} -\usepackage[T1]{fontenc} -\usepackage{graphicx} -\usepackage{grffile} -\usepackage{longtable} -\usepackage{wrapfig} -\usepackage{rotating} -\usepackage[normalem]{ulem} -\usepackage{amsmath} -\usepackage{textcomp} -\usepackage{amssymb} -\usepackage{capt-of} -\usepackage{hyperref} -\author{Philipp Homan} -\date{\today} -\title{} -\begin{document} - -\tableofcontents - -\end{document}