Improved graphics

src/beamerthemeph.sty

@@ -106,7 +106,7 @@
   \leavevmode
   \begin{columns}[t,onlytextwidth]
 	\column{.87\textwidth}
-	  \begin{beamercolorbox}[wd=\columnwidth, leftskip=2.0cm]{headline}
+	  \begin{beamercolorbox}[wd=\columnwidth, leftskip=2.0cm, ht=11.55cm]{headline}
 %  	\vskip1.5cm
 %		\centering
      \vskip7.6ex

src/org-mode-poster_poster.org

@@ -1,6 +1,5 @@
 #+startup: beamer
-#+TITLE: A scientific poster entirely written in org-mode 
+#+TITLE: Using org-mode to produce scientific posters 
-#+TITLE: using GNU emacs and the beamer library
 * Preamble                                                    :ignore:
 ** General comments                                           :ignore:
 # ----------------------------------------------------------------------
@@ -138,15 +137,14 @@
 :BEAMER_env: fullframe
 :END:
 ** Code                                                       :ignore:
-# Babel code can go here to populate the poster with dynamic output from
+# Babel code can go here to populate the poster with dynamic output 
-# statistical calculations
 
-** Left column                                                  :BMCOL:
+** Left column                                        :BMCOL:
 :PROPERTIES:
 :BEAMER_col: 0.45
 :BEAMER_opt: [t]
 :END:
-*** Background                                                 :B_block:
+*** Background                                        :B_block:
 :PROPERTIES:
 :BEAMER_env: block
 :END:
@@ -168,17 +166,17 @@
 :END:
 
 #+NAME: code1
-#+BEGIN_SRC R :session :export both :results output graphics :file 3.png 
+#+BEGIN_SRC R  :file 3.png :session :exports both :results graphics  
-x <- rnorm(100, 0, 1)
+set.seed(20180402)
-hist(x, col="gray")
+x1 <- rnorm(100, 0, 1)
+x2 <- rnorm(100, 0.5, 1)
+hist(x1, col="red")
+hist(x2, col="blue", add=TRUE)
 #+END_SRC
 
-#+RESULTS: code1
-[[file:3.png]]
-
-
 #+NAME: figcode1
 #+CAPTION: This is the output.
+#+RESULTS: code1
 [[file:3.png]]
 
 *** Inline code and tables                            :B_block:
@@ -188,46 +186,51 @@ hist(x, col="gray")
 - 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
+- Some code to process the first vector from above to make a table out
-  summary could look like this, which would result in a little table
+  of its summary could look like this, which would result in a little
-  (Table [[tabcode2]]) :
+  table (Table [[tabcode2]]) :
 
 **** Block
 :PROPERTIES:
-:BEAMER_col: 0.48
+:BEAMER_col: 0.88
 :BEAMER_opt: [T]
 :END:
 
 #+NAME: code2
 #+BEGIN_SRC R :session :exports both :results value :colnames yes :cache yes
-m <- round(mean(x), 2)
+library(broom)
-s <- round(sd(x), 2)
+library(dplyr)
-data.frame(Mean=m, SD=s)
+t1 <- tidy(round(summary(x1), 2)) 
+t2 <- tidy(round(summary(x2), 2))
+
+# This will export as a table
+rbind(t1, t2) %>%
+mutate(name=c("x1", "x2"))
 #+END_SRC
 
 \vspace{2cm}
 
-#+CAPTION: A table.
+#+CAPTION: A table summarizing the two distributions.
 #+NAME: tabcode2
-#+RESULTS[31e41e0f8cc2db2fb601af81fe4f5e218ea48f57]: code2
+#+RESULTS[9d0ec7348265a5cb6de39440ff06a8dbb8e5ecf1]: code2
-|-------+------|
+|---------+-------+--------+------+------+---------+------|
-|  Mean |   SD |
+| minimum |    q1 | median | mean |   q3 | maximum | name |
-|-------+------|
+|---------+-------+--------+------+------+---------+------|
-| -0.07 | 0.97 |
+|   -2.29 | -0.49 |   0.11 | 0.14 |  0.8 |    2.47 | x1   |
-|-------+------|
+|   -2.17 | -0.45 |   0.07 | 0.13 | 0.85 |    2.23 | x2   |
+|---------+-------+--------+------+------+---------+------|
 
-** Right column                                                 :BMCOL:
+** Right column                                       :BMCOL:
 :PROPERTIES:
 :BEAMER_col: 0.45
 :BEAMER_opt: [t]
 :END:
-*** Graphics                                                    :B_block:
+*** Graphics                                          :B_block:
 :PROPERTIES:
 :BEAMER_env: block
 :END:
 
-- Of course we can also include graphics
+- We can use shell scripting to grab an image with curl from the
-- Here, we use shell scripting to grab an image with curl from the
   internet (Fig. [[figcode3]]):
 
 **** Block
@@ -239,6 +242,7 @@ data.frame(Mean=m, SD=s)
 \footnotesize
 #+NAME: code3
 #+BEGIN_SRC bash :exports both :file emacs.png  
+# Download emacs icon from gnu.org
 curl -0 https://www.gnu.org/software/emacs/images/emacs.png
 #+END_SRC
 \normalsize
@@ -251,12 +255,14 @@ curl -0 https://www.gnu.org/software/emacs/images/emacs.png
 #+RESULTS: code3
 [[file:emacs.png]]
 
-*** Math                                                        :B_block:
+*** Math                                                   :B_block:
 :PROPERTIES:
 :BEAMER_env: block
 :END:
 
-- We can easily include math: 
+- We can easily include math
+- For example, let's describe how to compute the distance between the
+  two simulated distributions $x1$ and $x2$ from before:
 
 **** Block
 :PROPERTIES:
@@ -284,7 +290,7 @@ derived as follows:
 \DKLPQ{P}{Q}{,} = \sumin \Big(\Xoi{P} \log \frakPQ{P}{Q} + \Xoi{Q} \log \frakPQ{Q}{P} \Big).
 \end{align}
 
-*** Columns                                                     :B_block:
+*** Columns                                                :B_block:
 :PROPERTIES:
 :BEAMER_env: block
 :END:
@@ -295,11 +301,19 @@ derived as follows:
 :BEAMER_opt: [T]
 :END:
 
-\captionsetup{justification=justified,width=.8\linewidth}
+#+NAME: codeleft
-#+NAME: figge
+#+BEGIN_SRC R :file 4l.png :session org_org :exports results :results graphics
-#+CAPTION: *This is the left figure of a two-column block*
+d1 <- density(x1)
-#+ATTR_LATEX: :width 0.9\textwidth :options page=3
+plot(d1, col="red", lwd=3)
-[[file:org-mode-poster-4.png]]
+#+END_SRC
+
+
+\captionsetup{justification=justified,width=.85\linewidth}
+#+NAME: figcodeleft
+#+CAPTION: This is the left figure of a two-column block, showing
+#+CAPTION: the density of $x1$.
+#+RESULTS: codeleft
+[[file:4l.png]]
 
 **** Right
 :PROPERTIES:
@@ -307,16 +321,22 @@ derived as follows:
 :BEAMER_opt: [T]
 :END:
 
-\captionsetup{justification=justified,width=.8\linewidth}
+#+NAME: coderight
-#+NAME: figclus
+#+BEGIN_SRC R  :file 4r.png :session org_org :exports results :results graphics
-#+CAPTION: *This is the right figure.*
+d2 <- density(x2)
-#+ATTR_LATEX: :width 0.9\textwidth :options page=9
+plot(d2, col="blue", lwd=3)
-[[file:org-mode-poster-4.png]]
+#+END_SRC
 
-*** Conclusions                                                :B_block:
+\captionsetup{justification=justified,width=.85\linewidth}
+#+NAME: figcoderight
+#+CAPTION: This is the right figure. It shows the density of $x2$.
+#+RESULTS: coderight
+[[file:4r.png]]
+
+*** Conclusions                                            :B_block:
 :PROPERTIES:
 :BEAMER_env: block
 :END:
 - This little example is meant to show how incredibly versatile
   org-mode is 
-- One can now produce scientific posters with a simple text editor 
+- Scientific posters can be produced with a simple text editor 

src/org-mode-poster_poster.tex

@@ -1,4 +1,4 @@
-% Created 2018-04-02 Mon 18:38
+% Created 2018-04-02 Mon 19:58
 % Intended LaTeX compiler: pdflatex
 \documentclass[final]{beamer}
 	         \usetheme{ph}
@@ -33,11 +33,11 @@ Philipp Homan$^{1}$,
 \normalsize{Hempstead, NY}
 }
 \usetheme{default}
-\date{2018-04-02 18:38}
+\date{2018-04-02 19:58}
-\title{A scientific poster entirely written in org-mode using GNU emacs and the beamer library}
+\title{Using org-mode to produce scientific posters}
 \begin{document}
 
-\begin{frame}[fragile,label={sec:org727f6f5}]{}
+\begin{frame}[fragile,label={sec:org10a116a}]{}
  \begin{columns}
 \begin{column}[t]{0.45\columnwidth}
 \begin{block}{Background}
@@ -51,21 +51,23 @@ org-mode syntax
 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:orgaca79ae}):
+(Fig. \ref{fig:org8cce396}):
 \end{itemize}
 
 \begin{columns}
 \begin{column}[T]{0.48\columnwidth}
 \begin{minted}[linenos=true]{r}
-x <- rnorm(100, 0, 1)
+set.seed(20180402)
-hist(x, col="gray")
+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:orgaca79ae}
+\caption{\label{fig:org8cce396}
 This is the output.}
 \end{figure}
 \end{column}
@@ -77,30 +79,38 @@ This is the output.}
 \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 vector from above to make a table out of its
+\item Some code to process the first vector from above to make a table out
-summary could look like this, which would result in a little table
+of its summary could look like this, which would result in a little
-(Table \ref{tab:org6921627}) :
+table (Table \ref{tab:orgfdd29a9}) :
 \end{itemize}
 
 \begin{columns}
-\begin{column}[T]{0.48\columnwidth}
+\begin{column}[T]{0.88\columnwidth}
 \begin{minted}[linenos=true]{r}
-m <- round(mean(x), 2)
+library(broom)
-s <- round(sd(x), 2)
+library(dplyr)
-data.frame(Mean=m, SD=s)
+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}{rr}
+\begin{tabular}{rrrrrrl}
-Mean & SD\\
+\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
-0.07 & 0.98\\
 \end{tabular}
-\caption{\label{tab:org6921627}
+\caption{\label{tab:orgfdd29a9}
-A table.}
+A table summarizing the two distributions.}
 
 \end{table}
 \end{column}
@@ -111,15 +121,15 @@ A table.}
 \begin{column}[t]{0.45\columnwidth}
 \begin{block}{Graphics}
 \begin{itemize}
-\item Of course we can also include graphics
+\item We can use shell scripting to grab an image with curl from the
-\item Here, we use shell scripting to grab an image with curl from the
+internet (Fig. \ref{fig:orga373a15}):
-internet (Fig. \ref{fig:orgf35b3ea}):
 \end{itemize}
 
 \begin{columns}
 \begin{column}[T]{0.78\columnwidth}
 \footnotesize
 \begin{minted}[linenos=true]{bash}
+# Download emacs icon from gnu.org
 curl -0 https://www.gnu.org/software/emacs/images/emacs.png
 \end{minted}
 \normalsize
@@ -129,7 +139,7 @@ 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:orgf35b3ea}
+\caption{\label{fig:orga373a15}
 This is the downloaded image.}
 \end{figure}
 \end{column}
@@ -138,7 +148,9 @@ This is the downloaded image.}
 
 \begin{block}{Math}
 \begin{itemize}
-\item We can easily include math:
+\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}
@@ -169,22 +181,22 @@ derived as follows:
 \begin{block}{Columns}
 \begin{columns}
 \begin{column}[T]{0.48\columnwidth}
-\captionsetup{justification=justified,width=.8\linewidth}
+\captionsetup{justification=justified,width=.85\linewidth}
 \begin{figure}[htbp]
 \centering
-\includegraphics[page=3,width=0.9\textwidth]{org-mode-poster-4.png}
+\includegraphics[width=.9\linewidth]{4l.png}
-\caption{\label{fig:org623938b}
+\caption{\label{fig:orgf47550b}
-\textbf{This is the left figure of a two-column block}}
+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=.8\linewidth}
+\captionsetup{justification=justified,width=.85\linewidth}
 \begin{figure}[htbp]
 \centering
-\includegraphics[page=9,width=0.9\textwidth]{org-mode-poster-4.png}
+\includegraphics[width=.9\linewidth]{4r.png}
-\caption{\label{fig:orgb76a1ef}
+\caption{\label{fig:org96112b0}
-\textbf{This is the right figure.}}
+This is the right figure. It shows the density of \(x2\).}
 \end{figure}
 \end{column}
 \end{columns}
@@ -194,7 +206,7 @@ derived as follows:
 \begin{itemize}
 \item This little example is meant to show how incredibly versatile
 org-mode is
-\item One can now produce scientific posters with a simple text editor
+\item Scientific posters can be produced with a simple text editor
 \end{itemize}
 \end{block}
 \end{column}

src/org-mode-poster_poster.tex~

@@ -1,4 +1,4 @@
-% Created 2018-04-02 Mon 18:37
+% Created 2018-04-02 Mon 19:58
 % Intended LaTeX compiler: pdflatex
 \documentclass[final]{beamer}
 	         \usetheme{ph}
@@ -33,11 +33,11 @@ Philipp Homan$^{1}$,
 \normalsize{Hempstead, NY}
 }
 \usetheme{default}
-\date{2018-04-02 18:37}
+\date{2018-04-02 19:58}
-\title{A scientific poster entirely written in org-mode using GNU emacs and the beamer library}
+\title{Using org-mode to produce scientific posters}
 \begin{document}
 
-\begin{frame}[fragile,label={sec:org4b06f5e}]{}
+\begin{frame}[fragile,label={sec:org5deb971}]{}
  \begin{columns}
 \begin{column}[t]{0.45\columnwidth}
 \begin{block}{Background}
@@ -51,21 +51,23 @@ org-mode syntax
 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:org042638b}):
+(Fig. \ref{fig:org71455a2}):
 \end{itemize}
 
 \begin{columns}
 \begin{column}[T]{0.48\columnwidth}
 \begin{minted}[linenos=true]{r}
-x <- rnorm(100, 0, 1)
+set.seet(20180402)
-hist(x, col="gray")
+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:org042638b}
+\caption{\label{fig:org71455a2}
 This is the output.}
 \end{figure}
 \end{column}
@@ -77,30 +79,38 @@ This is the output.}
 \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 vector from above to make a table out of its
+\item Some code to process the first vector from above to make a table out
-summary could look like this, which would result in a little table
+of its summary could look like this, which would result in a little
-(Table \ref{tab:orge51644d}) :
+table (Table \ref{tab:orgf4d0fa2}) :
 \end{itemize}
 
 \begin{columns}
-\begin{column}[T]{0.48\columnwidth}
+\begin{column}[T]{0.88\columnwidth}
 \begin{minted}[linenos=true]{r}
-m <- round(mean(x), 2)
+library(broom)
-s <- round(sd(x), 2)
+library(dplyr)
-data.frame(Mean=m, SD=s)
+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}{rr}
+\begin{tabular}{rrrrrrl}
-Mean & SD\\
+\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
-0.23 & 1.07\\
 \end{tabular}
-\caption{\label{tab:orge51644d}
+\caption{\label{tab:orgf4d0fa2}
-A table.}
+A table summarizing the two distributions.}
 
 \end{table}
 \end{column}
@@ -111,15 +121,15 @@ A table.}
 \begin{column}[t]{0.45\columnwidth}
 \begin{block}{Graphics}
 \begin{itemize}
-\item Of course we can also include graphics
+\item We can use shell scripting to grab an image with curl from the
-\item Here, we use shell scripting to grab an image with curl from the
+internet (Fig. \ref{fig:org5863a78}):
-internet (Fig. \ref{fig:orga669d9a}):
 \end{itemize}
 
 \begin{columns}
 \begin{column}[T]{0.78\columnwidth}
 \footnotesize
 \begin{minted}[linenos=true]{bash}
+# Download emacs icon from gnu.org
 curl -0 https://www.gnu.org/software/emacs/images/emacs.png
 \end{minted}
 \normalsize
@@ -129,7 +139,7 @@ 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:orga669d9a}
+\caption{\label{fig:org5863a78}
 This is the downloaded image.}
 \end{figure}
 \end{column}
@@ -138,7 +148,9 @@ This is the downloaded image.}
 
 \begin{block}{Math}
 \begin{itemize}
-\item We can easily include math:
+\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}
@@ -157,6 +169,11 @@ 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}
@@ -164,22 +181,22 @@ derived as follows:
 \begin{block}{Columns}
 \begin{columns}
 \begin{column}[T]{0.48\columnwidth}
-\captionsetup{justification=justified,width=.8\linewidth}
+\captionsetup{justification=justified,width=.85\linewidth}
 \begin{figure}[htbp]
 \centering
-\includegraphics[page=3,width=0.9\textwidth]{org-mode-poster-4.png}
+\includegraphics[width=.9\linewidth]{4l.png}
-\caption{\label{fig:org88ad0c6}
+\caption{\label{fig:orga83a496}
-\textbf{This is the left figure of a two-column block}}
+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=.8\linewidth}
+\captionsetup{justification=justified,width=.85\linewidth}
 \begin{figure}[htbp]
 \centering
-\includegraphics[page=9,width=0.9\textwidth]{org-mode-poster-4.png}
+\includegraphics[width=.9\linewidth]{4r.png}
-\caption{\label{fig:org9e1f136}
+\caption{\label{fig:org63d9981}
-\textbf{This is the right figure.}}
+This is the right figure. It shows the density of \(x2\).}
 \end{figure}
 \end{column}
 \end{columns}
@@ -189,7 +206,7 @@ derived as follows:
 \begin{itemize}
 \item This little example is meant to show how incredibly versatile
 org-mode is
-\item One can now produce scientific posters with a simple text editor
+\item Scientific posters can be produced with a simple text editor
 \end{itemize}
 \end{block}
 \end{column}