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Added poster

This commit is contained in:
Philipp Homan yoga ubuntu 17.10 2018-04-02 04:57:06 -04:00
parent b554831e1f
commit 77763ece3a
21 changed files with 3037 additions and 0 deletions
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%--------------------------------------------------------------------------------
% This style was created by Philipp Homan
% (Adaption from Rob J Hyndman and David Vilar)
% 4/1/18
%--------------------------------------------------------------------------------
\ProvidesPackage{beamerthemeph}
\selectcolormodel{cmyk}
\mode<presentation>
%--------------------------------------------------------------------------------
%--------------------------------------------------------------------------------
% custom colors
%--------------------------------------------------------------------------------
\definecolor{i6blue}{cmyk}{1,0.305,0,0.06}
\definecolor{i6bluedark}{rgb}{0.0156,0.2578,0.5625}
\definecolor{i6colorscheme1}{HTML}{FF6518} % e.g. for block title
%\definecolor{i6colorscheme1}{HTML}{FFFFFF} % e.g. for block title
%\definecolor{i6colorblockbg}{HTML}{0033cc}
%\definecolor{i6colorblockfg}{HTML}{FFFFFF}
\definecolor{i6colorblockfg}{HTML}{FCE94F}
%\definecolor{i6colorblockfg}{HTML}{0033cc}
\definecolor{i6colorblockbg}{HTML}{0033CC}
%\definecolor{i6colorblockbg}{HTML}{C3DFFF}
\definecolor{i6colorscheme2}{HTML}{000000} % e.g. title in headline
\definecolor{i6colorscheme3}{HTML}{C3DFFF} % e.g. for poster background
%\definecolor{i6colorscheme3}{HTML}{0033CC} % e.g. for poster background
\definecolor{i6colorscheme5}{HTML}{FFFFFF} % e.g. for poster background
\definecolor{i6colorscheme4}{HTML}{000000}
\definecolor{i6colorschemeHeadline}{HTML}{0033cc} % for headline bg
%\definecolor{i6colorschemeHeadline}{HTML}{FFFFFF} % for headline bg
%\definecolor{i6colorschemeFootline}{HTML}{100D09} % for headline bg
%--------------------------------------------------------------------------------
% headline colors and fonts
%--------------------------------------------------------------------------------
\setbeamercolor{headline}{fg=white,bg=i6colorschemeHeadline}
\setbeamercolor{title in headline}{fg=white}
\setbeamercolor{logo}{bg=white}
%\setbeamercolor{title in headline}{fg=blue}
%\setbeamercolor{author in headline}{fg=lightgray}
\setbeamercolor{author in headline}{fg=i6colorscheme3}
\setbeamercolor{institute in headline}{fg=lightgray}
\setbeamercolor{logo in headline}{fg=black,bg=lightgray}
\setbeamercolor{separation line}{bg=i6colorscheme1}
%--------------------------------------------------------------------------------
% footline colors and fonts
%--------------------------------------------------------------------------------
\setbeamercolor{footline}{fg=white,bg=i6colorschemeHeadline}
\setbeamerfont{footline}{fg=white, size=\normalsize}
%--------------------------------------------------------------------------------
% body colors and fonts
%--------------------------------------------------------------------------------
\setbeamercolor*{normal text}{fg=black,bg=i6colorscheme3}
%--------------------------------------------------------------------------------
% block environment
%--------------------------------------------------------------------------------
\setbeamercolor*{block body}{bg=i6colorscheme5,fg=black}
\setbeamerfont{block body}{size=\large}
\setbeamercolor*{block title}{fg=i6colorblockfg,bg=i6colorblockbg}
\setbeamerfont{block title}{size=\Large,series=\bf}
%--------------------------------------------------------------------------------
% example environment
%--------------------------------------------------------------------------------
\setbeamercolor*{example title}{fg=white,bg=i6colorscheme1}
\setbeamerfont{example title}{size=\large,series=\bf,bg=i6colorscheme1,fg=white}
\setbeamercolor{alerted text}{fg=i6colorscheme1}
\setbeamertemplate{itemize items}[circle]
\setbeamertemplate{navigation symbols}{} % no navigation on a poster
%--------------------------------------------------------------------------------
% caption
%--------------------------------------------------------------------------------
\setbeamerfont{caption name}{series=\bfseries,size={\small}}
\setbeamerfont{caption}{size={\small}}
\setbeamercolor{caption name}{fg=black}
%--------------------------------------------------------------------------------
% block
%--------------------------------------------------------------------------------
\setbeamertemplate{block begin}{
\vskip.75ex
\begin{beamercolorbox}[leftskip=1cm,colsep*=.75ex]{block title}%
\usebeamerfont*{block title}\Large\insertblocktitle
\end{beamercolorbox}%
{\ifbeamercolorempty[bg]{block body}{}{\nointerlineskip\vskip-0.5pt}}%
\usebeamerfont{block body}%
\begin{beamercolorbox}[colsep*=.75ex,sep=.75ex,vmode]{block body}%
\ifbeamercolorempty[bg]{block body}{\vskip-.25ex}{\vskip-.75ex}\vbox{}%
}
\setbeamertemplate{block end}{
\end{beamercolorbox}
}
%--------------------------------------------------------------------------------
%--------------------------------------------------------------------------------
% headline
%--------------------------------------------------------------------------------
\setbeamertemplate{headline}{
\leavevmode
\begin{columns}[t,onlytextwidth]
\column{.87\textwidth}
\begin{beamercolorbox}[wd=\columnwidth, leftskip=2.0cm]{headline}
% \vskip1.5cm
% \centering
\vskip7.6ex
\usebeamercolor{title in headline}{\color{fg}\textbf{\huge{\inserttitle}}\\[1ex]}
\usebeamercolor{author in headline}{\color{fg}\large{\insertauthor}\\[1ex]}
\vskip2.4ex
\end{beamercolorbox}
\column{.13\textwidth}
\begin{beamercolorbox}[wd=\columnwidth]{logo}
\centering
\vskip1.9cm
\includegraphics[width=0.8\linewidth]{logo.pdf}
\vskip1.9cm
\end{beamercolorbox}
\end{columns}
%\begin{beamercolorbox}[wd=\paperwidth]{lower separation line head}
% \rule{0pt}{2pt}
%\end{beamercolorbox}
%\begin{beamercolorbox}[wd=\paperwidth]{lower separation line head}
% \rule{0pt}{2pt}
%\end{beamercolorbox}
}
%--------------------------------------------------------------------------------
%--------------------------------------------------------------------------------
% Footer
%--------------------------------------------------------------------------------
\setbeamertemplate{footline}{
%\begin{beamercolorbox}[wd=\paperwidth]{upper separation line foot}
% \rule{0pt}{2pt}
%\end{beamercolorbox}
\begin{columns}[b,onlytextwidth]
\column{.35\textwidth}
\begin{beamercolorbox}[leftskip=-0.5cm,wd=\columnwidth]{logo}
\vskip3.25ex
\includegraphics[width=0.9\textwidth,right]{logo_feinstein.pdf}
\vskip1.6ex
\end{beamercolorbox}
\column{.65\textwidth}
\begin{beamercolorbox}[leftskip=1cm,wd=\columnwidth]{headline}
%\hfill \raisebox{-0.4cm}{\insertfooter}
\vskip1.5ex
%\insertfooter
\includegraphics[width=0.65\textwidth,left]{twittergithub.pdf}
\vskip1.5ex
%\begin{beamercolorbox}[wd=\columnwidth]{logo}
\end{beamercolorbox}
\end{columns}
%\begin{beamercolorbox}[wd=\paperwidth]{lower separation line head}
% \rule{0pt}{2pt}
%\end{beamercolorbox}
%\begin{beamercolorbox}[wd=\paperwidth]{lower separation line head}
% \rule{0pt}{2pt}
%\end{beamercolorbox}
}
%--------------------------------------------------------------------------------
\mode<all>
\setbeamertemplate{caption}[numbered]
\def\footer#1{\def\insertfooter{#1}}

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\relax
\providecommand\hyper@newdestlabel[2]{}
\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
\global\let\oldcontentsline\contentsline
\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global\let\oldnewlabel\newlabel
\gdef\newlabel#1#2{\newlabelxx{#1}#2}
\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\ifx\hyper@anchor\@undefined
\let\contentsline\oldcontentsline
\let\newlabel\oldnewlabel
\fi}
\fi}
\global\let\hyper@last\relax
\gdef\HyperFirstAtBeginDocument#1{#1}
\providecommand*\HyPL@Entry[1]{}
\HyPL@Entry{0<</P(1)>>}
\providecommand \oddpage@label [2]{}
\newlabel{sec:org8f3d3e7<1>}{{1}{1}{}{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {sec:org8f3d3e7<1>}{1}}
\newlabel{sec:org8f3d3e7}{{1}{1}{}{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {sec:org8f3d3e7}{1}}
\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
\newlabel{fig:orga7530f0}{{1}{1}{\textbf {This could be a figure.}\relax }{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {fig:orga7530f0}{1}}
\newlabel{fig:org95c7011}{{2}{1}{\textbf {This could be another figure.}\relax }{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {fig:org95c7011}{1}}
\newlabel{fig:org89b785d}{{3}{1}{\textbf {Another figure}\relax }{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {fig:org89b785d}{1}}
\newlabel{fig:org51482b3}{{4}{1}{\textbf {This is another figure}\relax }{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {fig:org51482b3}{1}}
\newlabel{fig:org2cc1106}{{5}{1}{\textbf {This is the right column of this box}\relax }{Doc-Start}{}}
\@writefile{snm}{\beamer@slide {fig:org2cc1106}{1}}
\@writefile{nav}{\headcommand {\slideentry {0}{0}{1}{1/1}{}{0}}}
\@writefile{nav}{\headcommand {\beamer@framepages {1}{1}}}
\@writefile{nav}{\headcommand {\beamer@partpages {1}{1}}}
\@writefile{nav}{\headcommand {\beamer@subsectionpages {1}{1}}}
\@writefile{nav}{\headcommand {\beamer@sectionpages {1}{1}}}
\@writefile{nav}{\headcommand {\beamer@documentpages {1}}}
\@writefile{nav}{\headcommand {\def \inserttotalframenumber {1}}}

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# Fdb version 3
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm
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INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmss17.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmss17.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmss17.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmsy10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/cm/cmex10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msam10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
INPUT /usr/share/texlive/texmf-dist/fonts/tfm/public/amsfonts/symbols/msbm10.tfm
INPUT ../lib/logo.pdf
INPUT ../lib/org-mode-poster-1.png
INPUT ../lib/org-mode-poster-2.png
INPUT ../lib/org-mode-poster-3.png
INPUT ../lib/org-mode-poster-4.png
INPUT ../lib/org-mode-poster-4.png
INPUT ../lib/logo.pdf
INPUT ../lib/logo_feinstein.pdf
INPUT ../lib/twittergithub.pdf
OUTPUT org-mode-poster_poster.nav
OUTPUT org-mode-poster_poster.toc
OUTPUT org-mode-poster_poster.snm
INPUT org-mode-poster_poster.aux

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\headcommand {\slideentry {0}{0}{1}{1/1}{}{0}}
\headcommand {\beamer@framepages {1}{1}}
\headcommand {\beamer@partpages {1}{1}}
\headcommand {\beamer@subsectionpages {1}{1}}
\headcommand {\beamer@sectionpages {1}{1}}
\headcommand {\beamer@documentpages {1}}
\headcommand {\def \inserttotalframenumber {1}}

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#+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{eurosym}
#+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
; 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\textwidth
: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 produce
decent looking scientific posters.
- We combine a relatively simple custom \LaTeX style file and common
org-mode syntax
*** Methods: Part 1 :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
\captionsetup{justification=justified,width=.85\linewidth}
#+NAME: figflowchart
#+CAPTION: *This could be a figure.*
#+ATTR_LATEX: :width 0.85\textwidth
[[file:org-mode-poster-1.png]]
*** Methods: Part 2 :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
\captionsetup{justification=justified,width=.85\linewidth}
#+NAME: figshrinkage
#+CAPTION: *This could be another figure.*
#+ATTR_LATEX: :width 0.85\textwidth
[[file:org-mode-poster-2.png]]
** Right column :BMCOL:
:PROPERTIES:
:BEAMER_col: 0.45\textwidth
:BEAMER_opt: [t]
:END:
*** Results: Part 1 :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
\captionsetup{justification=justified,width=.8\linewidth}
#+NAME: figplsbrains
#+CAPTION: *Another figure*
#+ATTR_LATEX: :width 0.8\textwidth
[[file:org-mode-poster-3.png]]
*** Results: Part 2 :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 another figure*
#+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 column of this box*
#+ATTR_LATEX: :width 0.9\textwidth :options page=9
[[file:org-mode-poster-4.png]]
*** Conclusions :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
- This example shows how incredibly versatile org-mode is. One can now
produce scientific posters with a text editor (preferably emacs).

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#+startup: beamer
#+TITLE: Structural similarity networks predict
#+TITLE: clinical outcome in early-phase schizophrenia
* 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: \usepackage[absolute,overlay]{textpos}
#+LATEX_HEADER: \graphicspath{{../output/figures/}{../lib/}}
#+LATEX_HEADER: \usepackage[export]{adjustbox}
#+LATEX_HEADER: \usepackage{graphicx,caption}
#+LATEX_HEADER: \usepackage{eurosym}
#+LATEX_HEADER: \usepackage{textcomp}
#+LATEX_HEADER: \usepackage{bibentry}
# LATEX_HEADER: \setlength{\TPVertModule}{1cm}
# LATEX_HEADER: \setlength{\oddsidemargin}{0.1in}
# LATEX_HEADER: \title{The demise of the spotted swamp frog}
# LATEX_HEADER: \author{Rob J Hyndman}
# LATEX_HEADER: \footer{
# LATEX_HEADER: \textbf{Philipp Homan, MD, PhD}\\
# LATEX_HEADER: phoman1@northwell.edu\\
# LATEX_HEADER: github.com/philipphoman}
#+LATEX_HEADER: \date{}
# ----------------------------------------------------------------------
** Authors and affiliations :ignore:
# ----------------------------------------------------------------------
#+LATEX_HEADER: \author{
#+LATEX_HEADER: Philipp Homan$^{1}$,
#+LATEX_HEADER: Miklos Argyelan$^{1}$,
#+LATEX_HEADER: Pamela DeRosse$^{1}$,
#+LATEX_HEADER: Delbert Robinson$^{1}$,
#+LATEX_HEADER: John M. Kane$^{1}$,
#+LATEX_HEADER: Todd Lencz$^{1}$,
#+LATEX_HEADER: Anil K. Malhotra$^{1}$
#+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
; 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:
# ----------------------------------------------------------------------
* References :ignore:
\bibliographystyle{nature}
\nobibliography{master}
* The poster
:PROPERTIES:
:BEGIN:
:BEAMER_env: fullframe
:END:
** Code :ignore:
# First, make sure all variables are availabe
#+HEADER: :exports none
#+BEGIN_SRC R :results silent :session
source("../src/fe_func.R")
source("../src/fe_load.R")
fef <- read.csv("../data/fe_cidar.csv")
feo <- read.csv("../data/fe_omega3.csv")
hca <- read.csv("../data/fe_hcm.csv")
# Load necessary results tables
roistab <- read.csv("../output/tables/fe_freesurfer_roinames.csv")
roitvalstab <- read.csv("../output/tables/fe_freesurfer_roitvals.csv")
permuttab <- read.csv("../output/tables/fe_msn_permut_rsq.csv")
bootstraptab <- read.csv("../output/tables/fe_msn_bootstrap_rsq.csv")
crossvaltab <- read.csv("../output/tables/fe_msn_crossvalidation.csv")
graphsumtab <- read.csv("../output/tables/fe_freesurfer_graphsum.csv")
plsrtab <- read.csv("../output/tables/fe_msn_plsscore_rs.csv")
deltadegreestab <- read.csv("../output/tables/fe_freesurfer_deltadegrees.csv")
# Custom functions
pvalstr <- function(pval) {
if (pval < 0.001) {
return("< 0.001")
} else {
return(paste("=", round(pval, 3)))
}
}
#+END_SRC
#+HEADER: :exports none
#+BEGIN_SRC R :results silent :session :cache yes
# Merge data sets and keep only interesting variables
# Rename variables for later
fefa <- fef %>% dplyr::filter(day==0&included16w==1) %>%
dplyr::mutate(study="CIDAR", group="SZ") %>%
dplyr::select(dup, iq, mccb, bprs, bprs_td, bprs_tdbl,
age, sex, race, hasmri, study, group,
education,
bmi, class, alcohol, drugs)
feoa <- feo %>% dplyr::filter(day==0&included16w==1) %>%
dplyr::mutate(study="Omega3", group="SZ") %>%
dplyr::select(dup, iq, mccb, bprs, bprs_td, bprs_tdbl,
age, sex, race, hasmri, study, group,
education,
bmi, class, alcohol, drugs)
#hca$male[hca$sex==1] <- 1
#hca$female[hca$sex==2] <- 1
hcab <- hca %>% dplyr::rename(age=age) %>%
filter(age<50) %>%
dplyr::select(sex, age, education, iq) %>%
dplyr::mutate(study="HC",
group="HC")
hcmeanage <- round(mean(hcab$age), 1)
hcsdage <- round(sd(hcab$age), 1)
hcmales <- sum(hcab$sex==1, na.rm=TRUE)
hcfemales <- sum(hcab$sex==2, na.rm=TRUE)
feffeo <- rbind(fefa, feoa) %>% filter(hasmri==1)
# Custom function
parse_agesex <- function() {
print(paste("(", n_females, " females; mean age [SD] = ",
meanage, " [", sdage, "])", sep=""))
}
parse_n <- function(group) {
switch(group,
sz={
print(paste("(/N/ = ", n_partic, ")", sep=""))
},
hc={
print(paste("(/N/ = ", n_partic_hc, ")", sep=""))
})
}
# R version
rvers <- version$version.string
# Python version
# pyvers <- system("python --version")
# pysurfvers <- system("pip freeze | grep pysurf")
#pyvers <- "2.7.13"
#pysurfvers <- "0.7"
pyplusvers <- system("pyv=$(python -V 2>&1); echo $pyv", intern=TRUE)
pysurfplusvers <- system("pip list | grep pysurf", intern=TRUE)
# Custom variables
n_nodes <- 2 * nlevels(roistab$name)
n_partic <- nrow(feffeo)
n_partic_hc <- nrow(hcab)
n_partic_full_bothsamples <- nrow(rbind(fef %>% filter(day==0),
feo %>% filter(day==0)))
n_females <- sum(feffeo$sex==1)
n_males <- sum(feffeo$sex==2)
meanage <- round(mean(feffeo$age, na.rm=TRUE), 1)
sdage <- round(sd(feffeo$age, na.rm=TRUE), 1)
# Cross validation values
cvkfold_k <- crossvaltab$k
cvrsq_mean <- crossvaltab$mean
cvrsq_sd <- crossvaltab$sd
# Permutation and bootstrap values
rsqorig <- unique(permuttab$rsq_orig)
npermut <- unique(permuttab$niter)
prsq_pval <- unique(permuttab$prsq_pva)
# PLS correlation values
pls1r <- plsrtab$r[plsrtab$component=="PLS1"]
pls1rpval <- plsrtab$pval[plsrtab$component=="PLS1"]
pls2r <- plsrtab$r[plsrtab$component=="PLS2"]
pls2rpval <- plsrtab$pval[plsrtab$component=="PLS2"]
# Graph summary, drop Cp and keep transitivity
# as the two are essential equal
graphsumtab <- graphsumtab %>% filter(metric!="Cp") %>%
mutate(metric=recode(metric,
transitivity="Cluster coef.",
diameter="Diameter",
E.global="Global efficiency",
E.local="Local efficiency",
num.hubs="Number of hubs",
richclub="Rich club coef.",
vulnerability="Vulnerability"))
#+END_SRC
** Left column :BMCOL:
:PROPERTIES:
:BEAMER_col: 0.45\textwidth
:BEAMER_opt: [t]
:END:
*** Background :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
- Schizophrenia has long been considered a disorder of dysconnectivity
in the brain
- Using graph theory, we computed statistical similarity networks for
each individual (Fig [[figflowchart]], [[figshrinkage]]) in two
early-phase schizophrenia cohorts src_R[:session]{parse_n("sz")}
{{{results((/N/ = 82))}}} and in healthy controls
src_R[:session]{parse_n("hc")} {{{results((/N/ = 77))}}} and tested
whether network architecture predicted treatment response
*** Methods: Structural similarity networks :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
\captionsetup{justification=justified,width=.85\linewidth}
#+NAME: figflowchart
#+CAPTION: *Analysis flow chart.*
#+CAPTION: The similarity between any pair of region was
#+CAPTION: estimated by calculating the
#+CAPTION: Kullback-Leibler (KL) divergence of their
#+CAPTION: probability distributions, resulting in
#+CAPTION: a similarity matrix.
#+CAPTION: The similarity matrix
#+CAPTION: was then thresholded into a binary matrix to
#+CAPTION: create a network graph. Graph-based
#+CAPTION: degree (or hubness) for each node was then
#+CAPTION: calculated for each individual participant.
#+CAPTION: Nodal degrees were then entered as
#+CAPTION: predictors into a partial
#+CAPTION: least squares regression, using individual
#+CAPTION: treatment response slopes as outcome
#+CAPTION: measure.
#+ATTR_LATEX: :width 0.85\textwidth
[[file:fe_freesurfer_flowchart.pdf]]
*** Methods: Individual treatment response :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
\captionsetup{justification=justified,width=.85\linewidth}
#+NAME: figshrinkage
#+CAPTION: *Partial pooling to regularize individual response slopes.*
#+CAPTION: *A.* *Individual time courses for all participants*
#+CAPTION: *from the first schizophrenia cohort.*
#+CAPTION: Partial pooling regularized
#+CAPTION: the individual slopes, i.e., the influence
#+CAPTION: of outliers with only few assessments was attenuated.
#+CAPTION: *B.* *The partial pooling effect*
#+CAPTION: *is demonstrated by the individual responses being*
#+CAPTION: *pulled toward the average treatment effect.*
#+CAPTION: As a consequence, outliers are less influential.
#+CAPTION: *C, D.* The same is shown for the second schizophrenia
#+CAPTION: cohort.
#+CAPTION: Dotted ellipses indicate confidence regions for the
#+CAPTION: average treatment effect.
#+ATTR_LATEX: :width 0.85\textwidth
[[file:fe_freesurfer_shrinkage.pdf]]
** Right column :BMCOL:
:PROPERTIES:
:BEAMER_col: 0.45\textwidth
:BEAMER_opt: [t]
:END:
*** Results: Partial least squares regression :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
- Individual differences in the configuration of structural similarity
networks explained a significant proportion of variance in treatment
response (Fig. [[figplsbrains]])
- Exploratory analysis: increased clustering and decreased network
integration in patients compared to controls (Fig. [[figge]],
[[figclus]])
\captionsetup{justification=justified,width=.8\linewidth}
#+NAME: figplsbrains
#+CAPTION: *PLS scores with individual treatment*
#+CAPTION: *response and contribution of cortical nodes*
#+CAPTION: *in the schizophrenia cohort*
#+CAPTION: Nodal degree for each of
#+CAPTION: the src_R[:session]{n_nodes} {{{results(68)}}}
#+CAPTION: was entered into a partial least squares (PLS)
#+CAPTION: regression, with individual treatment response
#+CAPTION: slopes as outcome measure. The first two
#+CAPTION: PLS components explained a significant proportion
#+CAPTION: of variance in treatment response. *A, B.* The first
#+CAPTION: PLS component correlated most strongly with
#+CAPTION: nodal degree of orbito- and prefrontal cortices
#+CAPTION: and posterior cingulate cortex. Note that
#+CAPTION: more negative slopes meant better
#+CAPTION: treatment response.
#+CAPTION: *B, C.* The second PLS component correlated most
#+CAPTION: most strongly with superior temporal, precentral,
#+CAPTION: and middle cingulate brain areas.
#+ATTR_LATEX: :width 0.8\textwidth
[[file:fe_freesurfer_plsbrains.pdf]]
*** Results: Increased clustering in patients :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: *Decreased network integration in*
#+CAPTION: *schizophrenia patients compared to controls.*
#+CAPTION: Means with error bands
#+CAPTION: are shown.
#+CAPTION: Non-overlapping error bands
#+CAPTION: indicate significant group differences (/P/ < 0.05).
#+ATTR_LATEX: :width 0.9\textwidth :options page=3
[[file:fe_freesurfer_graphsum_individual.pdf]]
**** Right
:PROPERTIES:
:BEAMER_col: 0.48
:BEAMER_opt: [T]
:END:
\captionsetup{justification=justified,width=.8\linewidth}
#+NAME: figclus
#+CAPTION: *Increased clustering in schizophrenia patients*
#+CAPTION: *compared to controls.*
#+CAPTION: Means with error bands are shown.
#+CAPTION: Non-overlapping error bands
#+CAPTION: indicate significant group differences (/P/ < 0.05).
#+ATTR_LATEX: :width 0.9\textwidth :options page=9
[[file:fe_freesurfer_graphsum_individual.pdf]]
*** Conclusions :B_block:
:PROPERTIES:
:BEAMER_env: block
:END:
- These data suggest a potential link between brain network morphology
and clinical outcome in early-phase schizophrenia

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\beamer@slide {sec:org8f3d3e7<1>}{1}
\beamer@slide {sec:org8f3d3e7}{1}
\beamer@slide {fig:orga7530f0}{1}
\beamer@slide {fig:org95c7011}{1}
\beamer@slide {fig:org89b785d}{1}
\beamer@slide {fig:org51482b3}{1}
\beamer@slide {fig:org2cc1106}{1}

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% Created 2018-04-02 Mon 04:55
% Intended LaTeX compiler: pdflatex
\documentclass[final]{beamer}
\usetheme{ph}
\usepackage[orientation=portrait,size=a0,scale=1.4]{beamerposter}
\usepackage[absolute,overlay]{textpos}
\usepackage[authoryear]{natbib}
\setlength{\paperwidth}{36in}
\setlength{\paperheight}{48in}
\setlength{\textwidth}{0.98\paperwidth}
\setlength{\textheight}{0.98\paperheight}
\graphicspath{{../output/figures/}{../lib/}}
\usepackage[export]{adjustbox}
\usepackage{graphicx,caption}
\usepackage{eurosym}
\usepackage{textcomp}
\usepackage{bibentry}
\date{}
\author{
Philipp Homan$^{1}$,
\\
\normalsize{$^{1}$Department of Psychiatry,}
\normalsize{The Donald and Barbara Zucker}
\normalsize{School of Medicine at Northwell/Hofstra,}
\normalsize{Hempstead, NY}\\
}
\usetheme{default}
\date{2018-04-02 04:55}
\title{A scientific poster entirely written in org-mode using GNU emacs and the beamer library}
\begin{document}
\begin{frame}[label={sec:org8f3d3e7}]{}
\begin{columns}
\begin{column}[t]{0.45\textwidth\columnwidth}
\begin{block}{Background}
\begin{itemize}
\item Org-mode is not only useful for producing blog posts and even
scientific manuscripts; it is also perfectly suitable to produce
decent looking scientific posters.
\item We combine a relatively simple custom \LaTeX style file and common
org-mode syntax
\end{itemize}
\end{block}
\begin{block}{Methods: Part 1}
\captionsetup{justification=justified,width=.85\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[width=0.85\textwidth]{org-mode-poster-1.png}
\caption{\label{fig:orga7530f0}
\textbf{This could be a figure.}}
\end{figure}
\end{block}
\begin{block}{Methods: Part 2}
\captionsetup{justification=justified,width=.85\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[width=0.85\textwidth]{org-mode-poster-2.png}
\caption{\label{fig:org95c7011}
\textbf{This could be another figure.}}
\end{figure}
\end{block}
\end{column}
\begin{column}[t]{0.45\textwidth\columnwidth}
\begin{block}{Results: Part 1}
\captionsetup{justification=justified,width=.8\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[width=0.8\textwidth]{org-mode-poster-3.png}
\caption{\label{fig:org89b785d}
\textbf{Another figure}}
\end{figure}
\end{block}
\begin{block}{Results: Part 2}
\begin{columns}
\begin{column}[T]{0.48\columnwidth}
\captionsetup{justification=justified,width=.8\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[page=3,width=0.9\textwidth]{org-mode-poster-4.png}
\caption{\label{fig:org51482b3}
\textbf{This is another figure}}
\end{figure}
\end{column}
\begin{column}[T]{0.48\columnwidth}
\captionsetup{justification=justified,width=.8\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[page=9,width=0.9\textwidth]{org-mode-poster-4.png}
\caption{\label{fig:org2cc1106}
\textbf{This is the right column of this box}}
\end{figure}
\end{column}
\end{columns}
\end{block}
\begin{block}{Conclusions}
\begin{itemize}
\item This example shows how incredibly versatile org-mode is. One can now
produce scientific posters with a text editor (preferably emacs).
\end{itemize}
\end{block}
\end{column}
\end{columns}
\end{frame}
\end{document}

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% Created 2018-04-02 Mon 04:55
% Intended LaTeX compiler: pdflatex
\documentclass[final]{beamer}
\usetheme{ph}
\usepackage[orientation=portrait,size=a0,scale=1.4]{beamerposter}
\usepackage[absolute,overlay]{textpos}
\usepackage[authoryear]{natbib}
\setlength{\paperwidth}{36in}
\setlength{\paperheight}{48in}
\setlength{\textwidth}{0.98\paperwidth}
\setlength{\textheight}{0.98\paperheight}
\graphicspath{{../output/figures/}{../lib/}}
\usepackage[export]{adjustbox}
\usepackage{graphicx,caption}
\usepackage{eurosym}
\usepackage{textcomp}
\usepackage{bibentry}
\date{}
\author{
Philipp Homan$^{1}$,
\\
\normalsize{$^{1}$Department of Psychiatry,}
\normalsize{The Donald and Barbara Zucker}
\normalsize{School of Medicine at Northwell/Hofstra,}
\normalsize{Hempstead, NY}\\
}
\usetheme{default}
\date{2018-04-02 04:55}
\title{A scientific poster entirely written in org-mode using GNU emacs and the beamer library}
\begin{document}
\begin{frame}[label={sec:org1377f91}]{}
\begin{columns}
\begin{column}[t]{0.45\textwidth\columnwidth}
\begin{block}{Background}
\begin{itemize}
\item Org-mode is not only useful for producing blog posts and even
scientific manuscripts; it is also perfectly suitable to produce
decent looking scientific posters.
\item We combine a relatively simple custom \LaTeX style file and common
org-mode syntax
\end{itemize}
\end{block}
\begin{block}{Methods: Part 1}
\captionsetup{justification=justified,width=.85\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[width=0.85\textwidth]{org-mode-poster-1.png}
\caption{\label{fig:orgb1905be}
\textbf{This could be a figure.}}
\end{figure}
\end{block}
\begin{block}{Methods: Part 2}
\captionsetup{justification=justified,width=.85\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[width=0.85\textwidth]{org-mode-poster-2.png}
\caption{\label{fig:org66f9b35}
\textbf{This could be another figure.}}
\end{figure}
\end{block}
\end{column}
\begin{column}[t]{0.45\textwidth\columnwidth}
\begin{block}{Results: Part 1}
\captionsetup{justification=justified,width=.8\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[width=0.8\textwidth]{org-mode-poster-3.png}
\caption{\label{fig:org4dea716}
\textbf{Another figure}}
\end{figure}
\end{block}
\begin{block}{Results: Part 2}
\begin{columns}
\begin{column}[T]{0.48\columnwidth}
\captionsetup{justification=justified,width=.8\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[page=3,width=0.9\textwidth]{org-mode-poster-4.png}
\caption{\label{fig:orgca84fda}
\textbf{This is another figure}}
\end{figure}
\end{column}
\begin{column}[T]{0.48\columnwidth}
\captionsetup{justification=justified,width=.8\linewidth}
\begin{figure}[htbp]
\centering
\includegraphics[page=9,width=0.9\textwidth]{org-mode-poster-5.png}
\caption{\label{fig:orgc005403}
\textbf{This is the right column of this box}}
\end{figure}
\end{column}
\end{columns}
\end{block}
\begin{block}{Conclusions}
\begin{itemize}
\item This example shows how incredibly versatile org-mode is. One can now
produce scientific posters with a text editor (preferably emacs).
\end{itemize}
\end{block}
\end{column}
\end{columns}
\end{frame}
\end{document}

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