feat: Add a figure from Charles 2023 that represents the TAG definitions

figures/tag-definition-figure.tex

@@ -0,0 +1,3 @@
+\caption[Tandemly Arrayed Genes (TAG) definitions]{
+  Tandemly Arrayed Genes (TAG) definitions.
+}

figures/tag-definition.tex

@@ -0,0 +1,48 @@
+% TAG definitions
+% Figure inspired from fig. 1 Charles 2023 internship report
+
+\documentclass[tikz]{standalone}
+
+\usepackage{tikz}
+
+
+\begin{document}
+\usetikzlibrary{positioning}
+\usetikzlibrary{decorations.pathreplacing}
+
+  \tikzset{
+    dot/.style={fill=black, circle, inner sep=1.5pt},
+    nod/.style={sloped, at start, xshift=3mm, font=\scriptsize, above},
+}
+\begin{tikzpicture}[node distance=0.25]
+  \newcommand{\geneLength}{1}
+  \newcommand{\geneHalfHeight}{0.25}
+  % DNA line
+  \draw[-,very thick] (-6,0) to (6,0);
+  % Gene blocks
+  \node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange1) at (-5,0) {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green1) [right=of orange1] {};
+  \node[rectangle,fill=red,minimum height=0.5cm, minimum width=1cm] (red1) [right=of green1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green2) [right=of red1] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green3) [right=of green2] {};
+  \node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green4) [right=of green3] {};
+  \node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue1) [right=of green4] {};
+  \node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue2) [right=of blue1] {};
+  \node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange2) [right=of blue2] {};
+
+  % Homology links
+
+  \draw[-,orange, bend left=40] (orange1) to coordinate[dot] node[nod] {$\mathrm{TAG}_7$} (orange2);
+
+  \draw[-,green,bend right=40] (green1) to (green2)
+  (green2) to (green3)
+  (green3) to (green4);
+  \draw[-,green,bend left=40] (green1) to (green3)
+  (green1) to coordinate[dot] node[nod] {$\mathrm{TAG}_3$}(green4);
+  \draw[-,green,bend right=40] (green1) to (green2)
+  (green2) to (green4);
+
+  \draw[-,blue, bend left=40] (blue1) to  coordinate[dot] node[nod] {$\mathrm{TAG}_0$} (blue2);
+\end{tikzpicture}
+
+\end{document}

report.org

@@ -157,7 +157,13 @@ We apply a graph clustering algorithm on the graph in order to infer the gene fa
 FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
 **** Detection of TAGs
 The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
-For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user.
+For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Ref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
+#+begin_export latex
+\fladdfig{
+	\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
+	\caption[Schematic representation of TAG definitions]{\label{fig:tag-definitions} Schematic representation of TAG definitions. Several genes are represented on a linear chromosome. The red box represent a singleton gene. Orange boxes represent a TAG with two duplicate genes seperated by 7 other genes ($\mathrm{TAG}_7$). Four green boxes constitute a TAG, the gene at the extremities are seperated by three genes ($\mathrm{TAG}_3$. The two blue boxes represents a TAG with two genes next to each other $\mathrm{TAG}_0$. The bended edges represents the homology links between each pair of genes of a TAG.}}
+#+end_export
+
 * Objectives for the internship
 ** Scientific questions
 The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.