From 822737bc69bad7e50dad050e79ba57e1b3bf9fb8 Mon Sep 17 00:00:00 2001 From: "Philipp Homan yoga ubuntu 17.10" Date: Thu, 5 Apr 2018 16:08:34 +0200 Subject: [PATCH] Cleaned up --- src/.#org-mode-poster_poster.org | 1 - ...8527206BDF2FB9743A1FCD8E321435A60EC.pygtex | 7 - ...8AD7ECE1161BED6D70335945ACD46C35809.pygtex | 4 - ...FEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex | 10 - .../default-pyg-prefix.pygstyle | 101 -- .../default.pygstyle | 101 -- src/org-mode-poster_poster.1.vrb | 173 -- src/org-mode-poster_poster.aux | 51 - src/org-mode-poster_poster.bbl | 0 src/org-mode-poster_poster.blg | 48 - src/org-mode-poster_poster.fdb_latexmk | 233 --- src/org-mode-poster_poster.fls | 456 ------ src/org-mode-poster_poster.log | 1395 ----------------- src/org-mode-poster_poster.nav | 7 - src/org-mode-poster_poster.org | 1 + src/org-mode-poster_poster.org~ | 433 ----- src/org-mode-poster_poster.out | 0 src/org-mode-poster_poster.pdf | Bin 209251 -> 209373 bytes src/org-mode-poster_poster.snm | 9 - src/org-mode-poster_poster.tex | 24 +- src/org-mode-poster_poster.tex~ | 218 --- src/org-mode-poster_poster.toc | 0 src/org-mode-poster_poster.vrb | 77 - 23 files changed, 13 insertions(+), 3336 deletions(-) delete mode 120000 src/.#org-mode-poster_poster.org delete mode 100644 src/_minted-org-mode-poster_poster/4F50C45CD1733808924D80824FB708527206BDF2FB9743A1FCD8E321435A60EC.pygtex delete mode 100644 src/_minted-org-mode-poster_poster/960F98AC4966D313135E43FDA8CBB8AD7ECE1161BED6D70335945ACD46C35809.pygtex delete mode 100644 src/_minted-org-mode-poster_poster/F870F16C680A2900730ED6B4821BCFEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex delete mode 100644 src/_minted-org-mode-poster_poster/default-pyg-prefix.pygstyle delete mode 100644 src/_minted-org-mode-poster_poster/default.pygstyle delete mode 100644 src/org-mode-poster_poster.1.vrb delete mode 100644 src/org-mode-poster_poster.aux delete mode 100644 src/org-mode-poster_poster.bbl delete mode 100644 src/org-mode-poster_poster.blg delete mode 100644 src/org-mode-poster_poster.fdb_latexmk delete mode 100644 src/org-mode-poster_poster.fls delete mode 100644 src/org-mode-poster_poster.log delete mode 100644 src/org-mode-poster_poster.nav delete mode 100644 src/org-mode-poster_poster.org~ delete mode 100644 src/org-mode-poster_poster.out delete mode 100644 src/org-mode-poster_poster.snm delete mode 100644 src/org-mode-poster_poster.tex~ delete mode 100644 src/org-mode-poster_poster.toc delete mode 100644 src/org-mode-poster_poster.vrb diff --git a/src/.#org-mode-poster_poster.org b/src/.#org-mode-poster_poster.org deleted file mode 120000 index 9cbacc5..0000000 --- a/src/.#org-mode-poster_poster.org +++ /dev/null @@ -1 +0,0 @@ -homan@homan-Lenovo-YOGA-710-11IKB.3240:1522929731 \ No newline at end of file diff --git a/src/_minted-org-mode-poster_poster/4F50C45CD1733808924D80824FB708527206BDF2FB9743A1FCD8E321435A60EC.pygtex b/src/_minted-org-mode-poster_poster/4F50C45CD1733808924D80824FB708527206BDF2FB9743A1FCD8E321435A60EC.pygtex deleted file mode 100644 index 8615ec3..0000000 --- a/src/_minted-org-mode-poster_poster/4F50C45CD1733808924D80824FB708527206BDF2FB9743A1FCD8E321435A60EC.pygtex +++ /dev/null @@ -1,7 +0,0 @@ -\begin{Verbatim}[commandchars=\\\{\}] -\PYG{k+kp}{set.seed}\PYG{p}{(}\PYG{l+m}{20180402}\PYG{p}{)} -x1 \PYG{o}{\PYGZlt{}\PYGZhy{}} rnorm\PYG{p}{(}\PYG{l+m}{100}\PYG{p}{,} \PYG{l+m}{0}\PYG{p}{,} \PYG{l+m}{1}\PYG{p}{)} -x2 \PYG{o}{\PYGZlt{}\PYGZhy{}} rnorm\PYG{p}{(}\PYG{l+m}{100}\PYG{p}{,} \PYG{l+m}{0.5}\PYG{p}{,} \PYG{l+m}{1}\PYG{p}{)} -hist\PYG{p}{(}x1\PYG{p}{,} col\PYG{o}{=}\PYG{l+s}{\PYGZdq{}red\PYGZdq{}}\PYG{p}{)} -hist\PYG{p}{(}x2\PYG{p}{,} col\PYG{o}{=}\PYG{l+s}{\PYGZdq{}blue\PYGZdq{}}\PYG{p}{,} add\PYG{o}{=}\PYG{k+kc}{TRUE}\PYG{p}{)} -\end{Verbatim} diff --git a/src/_minted-org-mode-poster_poster/960F98AC4966D313135E43FDA8CBB8AD7ECE1161BED6D70335945ACD46C35809.pygtex b/src/_minted-org-mode-poster_poster/960F98AC4966D313135E43FDA8CBB8AD7ECE1161BED6D70335945ACD46C35809.pygtex deleted file mode 100644 index cbb822a..0000000 --- a/src/_minted-org-mode-poster_poster/960F98AC4966D313135E43FDA8CBB8AD7ECE1161BED6D70335945ACD46C35809.pygtex +++ /dev/null @@ -1,4 +0,0 @@ -\begin{Verbatim}[commandchars=\\\{\}] -\PYG{c+c1}{\PYGZsh{} Download emacs icon from gnu.org} -curl \PYGZhy{}0 https://www.gnu.org/software/emacs/images/emacs.png -\end{Verbatim} diff --git a/src/_minted-org-mode-poster_poster/F870F16C680A2900730ED6B4821BCFEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex b/src/_minted-org-mode-poster_poster/F870F16C680A2900730ED6B4821BCFEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex deleted file mode 100644 index 5193803..0000000 --- a/src/_minted-org-mode-poster_poster/F870F16C680A2900730ED6B4821BCFEC7206BDF2FB9743A1FCD8E321435A60EC.pygtex +++ /dev/null @@ -1,10 +0,0 @@ -\begin{Verbatim}[commandchars=\\\{\}] -\PYG{k+kn}{library}\PYG{p}{(}broom\PYG{p}{)} 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\let\PYG@ul=\relax \let\PYG@tc=\relax% - \let\PYG@bc=\relax \let\PYG@ff=\relax} -\def\PYG@tok#1{\csname PYG@tok@#1\endcsname} -\def\PYG@toks#1+{\ifx\relax#1\empty\else% - \PYG@tok{#1}\expandafter\PYG@toks\fi} -\def\PYG@do#1{\PYG@bc{\PYG@tc{\PYG@ul{% - \PYG@it{\PYG@bf{\PYG@ff{#1}}}}}}} -\def\PYG#1#2{\PYG@reset\PYG@toks#1+\relax+\PYG@do{#2}} - -\expandafter\def\csname PYG@tok@gd\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}} -\expandafter\def\csname PYG@tok@gu\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}} -\expandafter\def\csname PYG@tok@gt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}} -\expandafter\def\csname PYG@tok@gs\endcsname{\let\PYG@bf=\textbf} -\expandafter\def\csname PYG@tok@gr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}} -\expandafter\def\csname PYG@tok@cm\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} -\expandafter\def\csname 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PYG@tok@gi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}} -\expandafter\def\csname PYG@tok@gh\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}} -\expandafter\def\csname PYG@tok@ni\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.60,0.60,0.60}{##1}}} -\expandafter\def\csname PYG@tok@nl\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.63,0.00}{##1}}} -\expandafter\def\csname PYG@tok@nn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}} -\expandafter\def\csname PYG@tok@no\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.53,0.00,0.00}{##1}}} -\expandafter\def\csname PYG@tok@na\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.49,0.56,0.16}{##1}}} -\expandafter\def\csname PYG@tok@nb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@nc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}} -\expandafter\def\csname PYG@tok@nd\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}} -\expandafter\def\csname PYG@tok@ne\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.82,0.25,0.23}{##1}}} -\expandafter\def\csname PYG@tok@nf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}} -\expandafter\def\csname PYG@tok@si\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}} -\expandafter\def\csname PYG@tok@s2\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@nt\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@nv\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} -\expandafter\def\csname PYG@tok@s1\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@dl\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@ch\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} -\expandafter\def\csname PYG@tok@m\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} -\expandafter\def\csname PYG@tok@gp\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}} -\expandafter\def\csname PYG@tok@sh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@ow\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}} -\expandafter\def\csname PYG@tok@sx\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@bp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@c1\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} -\expandafter\def\csname PYG@tok@fm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}} -\expandafter\def\csname PYG@tok@o\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} -\expandafter\def\csname PYG@tok@kc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@c\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} -\expandafter\def\csname PYG@tok@mf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} -\expandafter\def\csname PYG@tok@err\endcsname{\def\PYG@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}} -\expandafter\def\csname PYG@tok@mb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} -\expandafter\def\csname PYG@tok@ss\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}} -\expandafter\def\csname PYG@tok@sr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}} -\expandafter\def\csname PYG@tok@mo\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} -\expandafter\def\csname PYG@tok@kd\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@mi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} -\expandafter\def\csname PYG@tok@kn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@cpf\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}} -\expandafter\def\csname PYG@tok@kr\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@s\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@kp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@w\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}} -\expandafter\def\csname PYG@tok@kt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.69,0.00,0.25}{##1}}} -\expandafter\def\csname PYG@tok@sc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@sb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@sa\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} -\expandafter\def\csname PYG@tok@k\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}} -\expandafter\def\csname PYG@tok@se\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.73,0.40,0.13}{##1}}} -\expandafter\def\csname PYG@tok@sd\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}} - -\def\PYGZbs{\char`\\} -\def\PYGZus{\char`\_} -\def\PYGZob{\char`\{} -\def\PYGZcb{\char`\}} -\def\PYGZca{\char`\^} -\def\PYGZam{\char`\&} -\def\PYGZlt{\char`\<} -\def\PYGZgt{\char`\>} -\def\PYGZsh{\char`\#} -\def\PYGZpc{\char`\%} -\def\PYGZdl{\char`\$} -\def\PYGZhy{\char`\-} -\def\PYGZsq{\char`\'} -\def\PYGZdq{\char`\"} -\def\PYGZti{\char`\~} -% for compatibility with earlier versions -\def\PYGZat{@} -\def\PYGZlb{[} -\def\PYGZrb{]} -\makeatother - diff --git a/src/_minted-org-mode-poster_poster/default.pygstyle b/src/_minted-org-mode-poster_poster/default.pygstyle deleted file mode 100644 index bf5e830..0000000 --- a/src/_minted-org-mode-poster_poster/default.pygstyle +++ /dev/null @@ -1,101 +0,0 @@ - -\makeatletter -\def\PYGdefault@reset{\let\PYGdefault@it=\relax \let\PYGdefault@bf=\relax% - \let\PYGdefault@ul=\relax \let\PYGdefault@tc=\relax% - \let\PYGdefault@bc=\relax \let\PYGdefault@ff=\relax} -\def\PYGdefault@tok#1{\csname PYGdefault@tok@#1\endcsname} -\def\PYGdefault@toks#1+{\ifx\relax#1\empty\else% - \PYGdefault@tok{#1}\expandafter\PYGdefault@toks\fi} -\def\PYGdefault@do#1{\PYGdefault@bc{\PYGdefault@tc{\PYGdefault@ul{% - \PYGdefault@it{\PYGdefault@bf{\PYGdefault@ff{#1}}}}}}} -\def\PYGdefault#1#2{\PYGdefault@reset\PYGdefault@toks#1+\relax+\PYGdefault@do{#2}} - -\expandafter\def\csname 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versions -\def\PYGdefaultZat{@} -\def\PYGdefaultZlb{[} -\def\PYGdefaultZrb{]} -\makeatother - diff --git a/src/org-mode-poster_poster.1.vrb b/src/org-mode-poster_poster.1.vrb deleted file mode 100644 index d9024c4..0000000 --- a/src/org-mode-poster_poster.1.vrb +++ /dev/null @@ -1,173 +0,0 @@ -\frametitle{} -\begin{columns} -\begin{column}[t]{0.45\columnwidth} -\begin{block}{Background} -\begin{itemize} -\item Here we show how org-mode (version -9.1.7) and emacs (version -25.2.2) can be used to make decent looking scientific -posters -\item 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 -\item For example, this poster was created on 2018-04-05 15:59 on -Ubuntu 17.10. -\item Inline code could look like this (which will produce a graph; -Fig. \ref{fig:orgd999323}): -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.68\columnwidth} -\begin{minted}[linenos=true,bgcolor=lightgray]{r} -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{minted} - -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{3.png} -\caption{\label{fig:orgd999323} -This is the output.} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Inline code and tables} -\begin{itemize} -\item In addition to inline code, we can also produce tables -\item Tables are very powerful in org-mode, they even include spreadsheet -capabilities -\item 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 \ref{tab:org3b1c59c}) : -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -\begin{minted}[linenos=true,bgcolor=lightgray]{r} -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{minted} - -\vspace{2cm} - -\begin{table}[htbp] -\caption{\label{tab:org3b1c59c} -A table summarizing the two distributions.} -\centering -\begin{tabular}{rrrrrrl} -\hline -minimum & q1 & median & mean & q3 & maximum & name\\ -\hline --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\\ -\hline -\end{tabular} -\end{table} -\end{column} -\end{columns} -\end{block} -\end{column} - -\begin{column}[t]{0.45\columnwidth} -\begin{block}{Graphics} -\begin{itemize} -\item We can use shell scripting to grab an image with curl from the -internet (Fig. \ref{fig:org5db1ca6}): -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -\footnotesize -\begin{minted}[linenos=true,bgcolor=lightgray]{bash} -# Download emacs icon from gnu.org -curl -0 https://www.gnu.org/software/emacs/images/emacs.png -\end{minted} -\normalsize - -\vspace{2cm} - -\begin{figure}[htbp] -\centering -\includegraphics[page=9,width=0.2\textwidth]{emacs.png} -\caption{\label{fig:org5db1ca6} -This is the downloaded image.} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Math} -\begin{itemize} -\item We can easily include math -\item For example, let's describe how to compute the distance between the -two simulated distributions \(x1\) and \(x2\) from before: -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -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} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Columns} -\begin{columns} -\begin{column}[T]{0.48\columnwidth} -\captionsetup{justification=justified,width=.85\linewidth} -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{4l.png} -\caption{\label{fig:org4d1aa8d} -This is the left figure of a two-column block, showing the density of \(x1\).} -\end{figure} -\end{column} - -\begin{column}[T]{0.48\columnwidth} -\captionsetup{justification=justified,width=.85\linewidth} -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{4r.png} -\caption{\label{fig:org46ae343} -This is the right figure. It shows the density of \(x2\).} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Conclusions} -\begin{itemize} -\item This little example is meant to show how versatile org-mode is -\item Scientific posters can be produced with a simple text editor -\end{itemize} -\end{block} -\end{column} -\end{columns} diff --git a/src/org-mode-poster_poster.aux b/src/org-mode-poster_poster.aux deleted file mode 100644 index 56492ce..0000000 --- a/src/org-mode-poster_poster.aux +++ /dev/null @@ -1,51 +0,0 @@ -\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<>} -\providecommand \oddpage@label [2]{} -\newlabel{sec:orgf567eda<1>}{{1}{1}{}{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {sec:orgf567eda<1>}{1}} -\newlabel{sec:orgf567eda}{{1}{1}{}{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {sec:orgf567eda}{1}} -\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}} -\newlabel{fig:orgd999323}{{1}{1}{This is the output.\relax }{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {fig:orgd999323}{1}} -\newlabel{tab:org3b1c59c}{{1}{1}{A table summarizing the two distributions.\relax }{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {tab:org3b1c59c}{1}} -\newlabel{fig:org5db1ca6}{{2}{1}{This is the downloaded image.\relax }{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {fig:org5db1ca6}{1}} -\@writefile{snm}{\beamer@slide {eq:KL}{1}} -\newlabel{eq:KL}{{1}{1}{}{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {eq:KL2}{1}} -\newlabel{eq:KL2}{{2}{1}{}{Doc-Start}{}} -\newlabel{fig:org4d1aa8d}{{3}{1}{This is the left figure of a two-column block, showing the density of \(x1\).\relax }{Doc-Start}{}} -\@writefile{snm}{\beamer@slide {fig:org4d1aa8d}{1}} -\newlabel{fig:org46ae343}{{4}{1}{This is the right figure. 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30270 multiletter control sequences out of 15000+600000 - 18338 words of font info for 114 fonts, out of 8000000 for 9000 - 14 hyphenation exceptions out of 8191 - 53i,25n,92p,812b,1571s stack positions out of 5000i,500n,10000p,200000b,80000s - -Output written on org-mode-poster_poster.pdf (1 page). diff --git a/src/org-mode-poster_poster.nav b/src/org-mode-poster_poster.nav deleted file mode 100644 index 2e0c158..0000000 --- a/src/org-mode-poster_poster.nav +++ /dev/null @@ -1,7 +0,0 @@ -\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}} diff --git a/src/org-mode-poster_poster.org b/src/org-mode-poster_poster.org index 8a8c27d..c20bf43 100644 --- a/src/org-mode-poster_poster.org +++ b/src/org-mode-poster_poster.org @@ -371,3 +371,4 @@ plot(d2, col="blue", lwd=3) - 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/org-mode-poster_poster.org~ b/src/org-mode-poster_poster.org~ deleted file mode 100644 index 7d8f5c5..0000000 --- a/src/org-mode-poster_poster.org~ +++ /dev/null @@ -1,433 +0,0 @@ -#+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 " 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 - - diff --git a/src/org-mode-poster_poster.out b/src/org-mode-poster_poster.out deleted file mode 100644 index e69de29..0000000 diff --git a/src/org-mode-poster_poster.pdf b/src/org-mode-poster_poster.pdf index 4ed41f7ca5eee957132caa2ce7aab596a275175a..fa429e14e5b21c6fe56d85757530a7ce632b9d5a 100644 GIT binary patch delta 31157 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zLuo%gbspVbjwQ~rZy1iw)L(KJ&iL}f7CUwU?@PaL=0v-&BHSyGf(aF`C6wKyvf)0( zeUYWqirYya%pUh{AdmLllL%Sgkxm`dG5$9`;a_URzaRyBW9xqz5=Krg9!_TFu*{5{ PY#hw6}{1} -\beamer@slide {sec:orgf567eda}{1} -\beamer@slide {fig:orgd999323}{1} -\beamer@slide {tab:org3b1c59c}{1} -\beamer@slide {fig:org5db1ca6}{1} -\beamer@slide {eq:KL}{1} -\beamer@slide {eq:KL2}{1} -\beamer@slide {fig:org4d1aa8d}{1} -\beamer@slide {fig:org46ae343}{1} diff --git a/src/org-mode-poster_poster.tex b/src/org-mode-poster_poster.tex index c7aabf7..19d07aa 100644 --- a/src/org-mode-poster_poster.tex +++ b/src/org-mode-poster_poster.tex @@ -1,4 +1,4 @@ -% Created 2018-04-05 Thu 15:59 +% Created 2018-04-05 Thu 16:07 % Intended LaTeX compiler: pdflatex \documentclass[final]{beamer} \usetheme{ph} @@ -37,11 +37,11 @@ Philipp Homan$^{1}$ \normalsize{Hempstead, NY} } \usetheme{default} -\date{2018-04-05 15:59} +\date{2018-04-05 16:07} \title{Using org-mode for scientific posters} \begin{document} -\begin{frame}[fragile,label={sec:orgf567eda}]{} +\begin{frame}[fragile,label={sec:org7ec99ec}]{} \begin{columns} \begin{column}[t]{0.45\columnwidth} \begin{block}{Background} @@ -53,10 +53,10 @@ posters \item 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 -\item For example, this poster was created on 2018-04-05 15:59 on +\item For example, this poster was created on 2018-04-05 16:07 on Ubuntu 17.10. \item Inline code could look like this (which will produce a graph; -Fig. \ref{fig:orgd999323}): +Fig. \ref{fig:org9802921}): \end{itemize} \begin{columns} @@ -72,7 +72,7 @@ hist(x2, col="blue", add=TRUE) \begin{figure}[htbp] \centering \includegraphics[width=.9\linewidth]{3.png} -\caption{\label{fig:orgd999323} +\caption{\label{fig:org9802921} This is the output.} \end{figure} \end{column} @@ -86,7 +86,7 @@ This is the output.} capabilities \item 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 \ref{tab:org3b1c59c}) : +table (Table \ref{tab:orgd48ea4b}) : \end{itemize} \begin{columns} @@ -105,7 +105,7 @@ mutate(name=c("x1", "x2")) \vspace{2cm} \begin{table}[htbp] -\caption{\label{tab:org3b1c59c} +\caption{\label{tab:orgd48ea4b} A table summarizing the two distributions.} \centering \begin{tabular}{rrrrrrl} @@ -126,7 +126,7 @@ minimum & q1 & median & mean & q3 & maximum & name\\ \begin{block}{Graphics} \begin{itemize} \item We can use shell scripting to grab an image with curl from the -internet (Fig. \ref{fig:org5db1ca6}): +internet (Fig. \ref{fig:orge74f4ee}): \end{itemize} \begin{columns} @@ -143,7 +143,7 @@ curl -0 https://www.gnu.org/software/emacs/images/emacs.png \begin{figure}[htbp] \centering \includegraphics[page=9,width=0.2\textwidth]{emacs.png} -\caption{\label{fig:org5db1ca6} +\caption{\label{fig:orge74f4ee} This is the downloaded image.} \end{figure} \end{column} @@ -189,7 +189,7 @@ derived as follows: \begin{figure}[htbp] \centering \includegraphics[width=.9\linewidth]{4l.png} -\caption{\label{fig:org4d1aa8d} +\caption{\label{fig:org16d62b9} This is the left figure of a two-column block, showing the density of \(x1\).} \end{figure} \end{column} @@ -199,7 +199,7 @@ This is the left figure of a two-column block, showing the density of \(x1\).} \begin{figure}[htbp] \centering \includegraphics[width=.9\linewidth]{4r.png} -\caption{\label{fig:org46ae343} +\caption{\label{fig:orgf50bc84} This is the right figure. It shows the density of \(x2\).} \end{figure} \end{column} diff --git a/src/org-mode-poster_poster.tex~ b/src/org-mode-poster_poster.tex~ deleted file mode 100644 index f48e0b5..0000000 --- a/src/org-mode-poster_poster.tex~ +++ /dev/null @@ -1,218 +0,0 @@ -% Created 2018-04-04 Wed 12:21 -% 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{minted} -\usepackage{eurosym} -\usepackage{listings} -\usepackage{textcomp} -\usepackage{bibentry} -\newcommand\sumin{\sum_{i=1}^{n}} -\newcommand{\Xoi}[1]{#1(i)} -\newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}} -\newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)} -\date{} -\newcommand{\auth}{Philipp Homan, MD, PhD} -\newcommand{\authemail}{phoman1@northwell.edu} -\newcommand{\authtwitter}{@philipphoman} -\newcommand{\authgithub}{github.com/philipphoman} -\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{2018-04-04 12:21} -\title{Using org-mode for scientific posters} -\begin{document} - -\begin{frame}[fragile,label={sec:org954d466}]{} - \begin{columns} -\begin{column}[t]{0.45\columnwidth} -\begin{block}{Background} -\begin{itemize} -\item Here we show how org-mode (version -9.1.7) and emacs (version -25.2.2) can be used to make decent looking scientific -posters -\item 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 -\item For example, this poster was created on 2018-04-04 12:21 on -Ubuntu 17.10. -\item Inline code could look like this (which will produce a graph; -Fig. \ref{fig:org8e3f41e}): -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.68\columnwidth} -\begin{minted}[linenos=true,bgcolor=lightgray]{r} -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{minted} - -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{3.png} -\caption{\label{fig:org8e3f41e} -This is the output.} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Inline code and tables} -\begin{itemize} -\item In addition to inline code, we can also produce tables -\item Tables are very powerful in org-mode, they even include spreadsheet -capabilities -\item 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 \ref{tab:orgd66dcb7}) : -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -\begin{minted}[linenos=true,bgcolor=lightgray]{r} -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{minted} - -\vspace{2cm} - -\begin{table}[htbp] -\caption{\label{tab:orgd66dcb7} -A table summarizing the two distributions.} -\centering -\begin{tabular}{rrrrrrl} -\hline -minimum & q1 & median & mean & q3 & maximum & name\\ -\hline --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\\ -\hline -\end{tabular} -\end{table} -\end{column} -\end{columns} -\end{block} -\end{column} - -\begin{column}[t]{0.45\columnwidth} -\begin{block}{Graphics} -\begin{itemize} -\item We can use shell scripting to grab an image with curl from the -internet (Fig. \ref{fig:orga7f94bb}): -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -\footnotesize -\begin{minted}[linenos=true,bgcolor=lightgray]{bash} -# Download emacs icon from gnu.org -curl -0 https://www.gnu.org/software/emacs/images/emacs.png -\end{minted} -\normalsize - -\vspace{2cm} - -\begin{figure}[htbp] -\centering -\includegraphics[page=9,width=0.2\textwidth]{emacs.png} -\caption{\label{fig:orga7f94bb} -This is the downloaded image.} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Math} -\begin{itemize} -\item We can easily include math -\item For example, let's describe how to compute the distance between the -two simulated distributions \(x1\) and \(x2\) from before: -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -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} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Columns} -\begin{columns} -\begin{column}[T]{0.48\columnwidth} -\captionsetup{justification=justified,width=.85\linewidth} -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{4l.png} -\caption{\label{fig:org0b56e4b} -This is the left figure of a two-column block, showing the density of \(x1\).} -\end{figure} -\end{column} - -\begin{column}[T]{0.48\columnwidth} -\captionsetup{justification=justified,width=.85\linewidth} -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{4r.png} -\caption{\label{fig:org5983ee2} -This is the right figure. It shows the density of \(x2\).} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Conclusions} -\begin{itemize} -\item This little example is meant to show how versatile org-mode is -\item Scientific posters can be produced with a simple text editor -\end{itemize} -\end{block} -\end{column} -\end{columns} -\end{frame} -\end{document} diff --git a/src/org-mode-poster_poster.toc b/src/org-mode-poster_poster.toc deleted file mode 100644 index e69de29..0000000 diff --git a/src/org-mode-poster_poster.vrb b/src/org-mode-poster_poster.vrb deleted file mode 100644 index b734c41..0000000 --- a/src/org-mode-poster_poster.vrb +++ /dev/null @@ -1,77 +0,0 @@ -,label={sec:org42c14b4}]{Left column} - \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 make -decent looking scientific posters -\item We combine a relatively simple custom \LaTeX style file and common -org-mode syntax -\item 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 -\item Inline code would look like this, which will produce a graph -(Fig. \ref{fig:orgb6e58a4}): -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.68\columnwidth} -\begin{minted}[linenos=true,bgcolor=lightgray]{r} -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{minted} - -\begin{figure}[htbp] -\centering -\includegraphics[width=.9\linewidth]{3.png} -\caption{\label{fig:orgb6e58a4} -This is the output.} -\end{figure} -\end{column} -\end{columns} -\end{block} - -\begin{block}{Inline code and tables} -\begin{itemize} -\item In addition to inline code, we can also produce tables -\item Tables are very powerful in org-mode, they even include spreadsheet -capabilities -\item 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 \ref{tab:org4e98e45}) : -\end{itemize} - -\begin{columns} -\begin{column}[T]{0.78\columnwidth} -\begin{minted}[linenos=true,bgcolor=lightgray]{r} -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{minted} - -\vspace{2cm} - -\begin{table}[htbp] -\centering -\begin{tabular}{rrrrrrl} -\hline -minimum & q1 & median & mean & q3 & maximum & name\\ -\hline --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\\ -\hline -\end{tabular} -\caption{\label{tab:org4e98e45} -A table summarizing the two distributions.} - -\end{table} -\end{column} -\end{columns} -\end{block}