Added some figures.

lectures/data_sharing/data_sharing.tex

@@ -23,26 +23,6 @@
 \section{Introduction}
 \makeTableOfContents
 
-\begin{pframe}
-  \begin{figure}[]
-    \begin{center}
-      \includegraphics[height=0.7\textheight]{gq}
-    \end{center}
-    \caption{}
-    \label{}
-  \end{figure}
-\end{pframe}
-
-\begin{pframe}
-  \begin{figure}[]
-    \begin{center}
-      \includegraphics[height=0.7\textheight]{samples}
-    \end{center}
-    \caption{}
-    \label{}
-  \end{figure}
-\end{pframe}
-
 \subsection{Types of variants}
 \begin{pframe}
   % Data sharing at the LUMC:
@@ -50,8 +30,6 @@
   % - Variant frequencies.
 \end{pframe}
 
-% Issues with sharing frequencies:
-% - See VKGL discussion.
 \subsection{Requirements}
 \begin{pframe}
   We aim for a solution that has the following properties:
@@ -73,6 +51,70 @@
   Timestamps are essential for \emph{reproducibility}.
 \end{pframe}
 
+\begin{pframe}
+  \begin{figure}[]
+    \vspace{-0.5cm}
+    \begin{center}
+      \includegraphics[height=0.8\textheight]{gq}
+    \end{center}
+    \vspace{-0.3cm}
+    \caption{Callable region ($584$--$1596$).}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \vspace{-0.5cm}
+    \begin{center}
+      \includegraphics[height=0.8\textheight]{samples}
+      \begin{picture}(0, 0)
+        \only<2>{\put(-45, 9.5){\line(0, 1){50}}}
+        \only<3>{\put(-23, 9.5){\line(0, 1){50}}}
+      \end{picture}
+    \end{center}
+    \vspace{-0.3cm}
+    \caption{Sharing observations is not enough.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \Large\texttt{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA}
+    \end{center}
+    \caption{\bt{NM\_003002.2:c.262\_266del}.}
+  \end{figure}
+
+  \begin{figure}[]
+    \begin{center}
+      \Large\texttt{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA}\\
+      \Large\texttt{TTGAATCCTT \color{red}GCTCT \color{black}GCGATGGA}\\
+      \Large\texttt{TTGAATCCTTG \color{red}CTCTG \color{black}CGATGGA}\\
+      \Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}
+    \end{center}
+    %\caption{\bt{NM\_003002.2:c.262\_266del}.}
+  \end{figure}
+
+  \begin{figure}[]
+    \begin{center}
+      \Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}
+    \end{center}
+    \caption{\bt{NM\_003002.2:c.265\_269del}.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      Genome\\
+      {\Large\texttt{AACTTAGGA \color{red}ACGAG \color{black}ACGCTACCT}}\\
+      {\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}}\\
+      Transcript
+    \end{center}
+    \caption{}
+  \end{figure}
+\end{pframe}
+
 \subsection{Options}
 \begin{pframe}
   Choices for the database layout:

lectures/data_sharing/generate.sh

+#!/bin/sh
+
+python gq.py '[(500, 1500)]' > gq_1.dat
+python gq.py '[(100, 600), (1000, 1600)]' > gq_2.dat
+python gq.py '[(1200, 1800)]' > gq_3.dat

lectures/data_sharing/gq.gnp

@@ -8,4 +8,4 @@ set multiplot
 set nokey
 plot "gq_1.dat" notitle
 set style data lines
-plot 30 lc 0 lw 8
+plot 30 lc 0 lw 10

lectures/data_sharing/gq.py

 #!/usr/bin/env python
 
 import random
+import sys
+
+
+coverage = eval(sys.argv[1])
+
+
+def target_coverage(position, coverage):
+    for c in coverage:
+        if c[0] <= position <= c[1]:
+            return 45
+    return 0
 
 
 y = 0
-for i in range(2000):
-    y = max(0, y + random.randint(-1, 1))
+for x in range(2000):
+    dy = random.randint(-1, 1)
+
+    t = target_coverage(x, coverage)
+    if not random.randint(0, 1):
+        if y > t + 5:
+            dy = min(0, dy)
+        if y < t - 5:
+            dy = max(0, dy)
+
+    y = max(0, y + dy)
     print y

lectures/data_sharing/gq_1.dat

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