From e8d9ccc8cead5281520d825138ddd5033064757c Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Sun, 18 Oct 2015 17:35:08 -0700
Subject: [PATCH] move usage around include example output center figures from
 the diamond paper

---
 diamond_presentation_2015.Rnw | 55 ++++++++++++++++++++++++++---------
 1 file changed, 41 insertions(+), 14 deletions(-)

diff --git a/diamond_presentation_2015.Rnw b/diamond_presentation_2015.Rnw
index 6a90f32..d6d307e 100644
--- a/diamond_presentation_2015.Rnw
+++ b/diamond_presentation_2015.Rnw
@@ -287,35 +287,62 @@ library("xtable")
   \end{itemize}
 \end{frame}
 
-\section{Usage}
-
-\begin{frame}{DIAMOND Usage}
-  \begin{itemize}
-  \item Make the diamond database: 
-    \texttt{diamond makedb --in foo.fasta --db foo.dmnd;}
-  \item Run the diamond query: 
-    \texttt{diamond blastx --db foo.diamond --threads 24 --query bar.fasta --daa bar\_diamond.txt}
-  \end{itemize}
-\end{frame}
-
 \section{Comparison}
 
 \subsection{Speed}
 
 \begin{frame}{Speed of DIAMOND}
-  \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_a.jpg}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_a.jpg}
+  \end{center}
 \end{frame}
 
 \subsection{Accuracy}
 
 \begin{frame}{Accuracy of DIAMOND: Any success}
-  \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_b.jpg}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_b.jpg}
+  \end{center}
 \end{frame}
 
 \begin{frame}{Accuracy of DIAMOND: Matches blastx}
-  \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_c.jpg}
+  \begin{center}
+    \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_c.jpg}
+  \end{center}
 \end{frame}
 
+\section{Usage}
+
+\begin{frame}{DIAMOND Usage}
+  \begin{itemize}
+  \item Make the diamond database: 
+    \texttt{diamond makedb --in foo.fasta --db foo.dmnd;}
+  \item Run the diamond query: 
+    \texttt{diamond blastx --db foo.diamond --threads 24 --query bar.fasta --daa bar\_diamond.txt}
+  \end{itemize}
+\end{frame}
+
+
+\subsection{Output}
+\begin{frame}{DIAMOND Output}
+  \begin{itemize}
+  \item Standard BLASTx output
+  \item Equivalent evalues and bit scores
+  \item An example from \textit{Spalax} (the top two proteins are
+    isoforms):
+  \end{itemize}
+  \tiny
+  \begin{tabular}{c c c c c c c c c c c c}
+    query & match & \% ident & length & \# mm & gap & qst & qstp & sstart & sstop & evalue & score \\
+c18\_g1\_i1 & ...065786 & 94.5 & 361 & 20 & 0 & 2 & 1084 & 992 & 1352 & 5.7e-203 & 704.9 \\
+c18\_g1\_i1 & ...081540 & 94.5 & 361 & 20 & 0 & 2 & 1084 & 940 & 1300 & 5.7e-203 & 704.9 \\
+c18\_g1\_i1 & ...142322 & 48.8 & 361 & 178 & 3 & 5 & 1078 & 944 & 1300 & 5.9e-99 & 359.4 \\
+c18\_g1\_i1 & ...039711 & 48.8 & 361 & 178 & 3 & 5 & 1078 & 936 & 1292 & 5.9e-99 & 359.4 \\
+c18\_g1\_i1 & ...141518 & 43.0 & 230 & 124 & 3 & 5 & 685 & 936 & 1161 & 1.7e-50 & 198.4 \\
+\end{tabular}
+\end{frame}
+
+
 
 \section*{References}
 
-- 
2.39.2