org-mode-poster/src/org-mode-poster_poster.org

#+startup: beamer
#+TITLE: A scientific poster entirely written in org-mode 
#+TITLE: using GNU emacs and the beamer library
* 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:
# ----------------------------------------------------------------------
** 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: \date{}
# ----------------------------------------------------------------------
** 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")))
  ; 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 "<f7> 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 from
# statistical calculations

** Left column                                                  :BMCOL:
:PROPERTIES:
:BEAMER_col: 0.45
:BEAMER_opt: [t]
:END:
*** Background                                                 :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
- Org-mode is not only useful for producing blog posts and even
  scientific manuscripts; it is also perfectly suitable to make 
  decent looking scientific posters
- We combine a relatively simple custom \LaTeX style file and common
  org-mode syntax
- The nice thing about org-mode is that we can populate the poster with
  code, graphs and numbers from inline code in languages such as R,
  python, Matlab and even shell scripting
- Inline code would look like this, which will produce a graph
  (Fig. [[figcode1]]):

**** Block
:PROPERTIES:
:BEAMER_col: 0.48
:BEAMER_opt: [T]
:END:

#+NAME: code1
#+BEGIN_SRC R :session :export both :results output graphics :file 3.png 
x <- rnorm(100, 0, 1)
hist(x, col="gray")
#+END_SRC

#+RESULTS: code1
[[file:3.png]]


#+NAME: figcode1
#+CAPTION: This is the output.
[[file:3.png]]

*** Methods: 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 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: 0.48
:BEAMER_opt: [T]
:END:

#+NAME: code2
#+BEGIN_SRC R :session :exports both :results value :colnames yes :cache yes
m <- round(mean(x), 2)
s <- round(sd(x), 2)
data.frame(Mean=m, SD=s)
#+END_SRC

\vspace{2cm}

#+CAPTION: A table.
#+NAME: tabcode2
#+RESULTS[31e41e0f8cc2db2fb601af81fe4f5e218ea48f57]: code2
|-------+------|
|  Mean |   SD |
|-------+------|
| -0.07 | 0.97 |
|-------+------|



** Right column                                                 :BMCOL:
:PROPERTIES:
:BEAMER_col: 0.45
:BEAMER_opt: [t]
:END:
*** Results: graphics                                          :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:

- Of course we can also include graphics
- Here, we use shell scripting to grab an image with curl from the
  internet (Fig. [[figcode3]]):

**** Block
:PROPERTIES:
:BEAMER_col: 0.78
:BEAMER_opt: [T]
:END:

\small
#+NAME: code3
#+BEGIN_SRC sh :exports both :file emacs.png  
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]]

*** Results: columns                                           :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:

**** Left
:PROPERTIES:
:BEAMER_col: 0.48
:BEAMER_opt: [T]
:END:

\captionsetup{justification=justified,width=.8\linewidth}
#+NAME: figge
#+CAPTION: *This is the left figure of a two-column block*
#+ATTR_LATEX: :width 0.9\textwidth :options page=3
[[file:org-mode-poster-4.png]]

**** Right
:PROPERTIES:
:BEAMER_col: 0.48
:BEAMER_opt: [T]
:END:

\captionsetup{justification=justified,width=.8\linewidth}
#+NAME: figclus
#+CAPTION: *This is the right figure.*
#+ATTR_LATEX: :width 0.9\textwidth :options page=9
[[file:org-mode-poster-4.png]]

*** Conclusions                                                :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
- This little example is meant to show how incredibly versatile
  org-mode is 
- One can now produce scientific posters with a simple text editor