From bb191d4cf741d63775be7bb2bcae3c94bc0245e4 Mon Sep 17 00:00:00 2001 From: Samuel Ortion Date: Tue, 16 Apr 2024 15:15:28 +0200 Subject: [PATCH] feat: Add a figure from Charles 2023 that represents the TAG definitions --- figures/tag-definition-figure.tex | 3 ++ figures/tag-definition.pdf | 3 ++ figures/tag-definition.tex | 48 +++++++++++++++++++++++++++++++ report.org | 8 +++++- report.pdf | 4 +-- 5 files changed, 63 insertions(+), 3 deletions(-) create mode 100644 figures/tag-definition-figure.tex create mode 100644 figures/tag-definition.pdf create mode 100644 figures/tag-definition.tex diff --git a/figures/tag-definition-figure.tex b/figures/tag-definition-figure.tex new file mode 100644 index 0000000..8733d21 --- /dev/null +++ b/figures/tag-definition-figure.tex @@ -0,0 +1,3 @@ +\caption[Tandemly Arrayed Genes (TAG) definitions]{ + Tandemly Arrayed Genes (TAG) definitions. +} diff --git a/figures/tag-definition.pdf b/figures/tag-definition.pdf new file mode 100644 index 0000000..7e243f7 --- /dev/null +++ b/figures/tag-definition.pdf @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d9731b10473b3a7a993729d14d316c2adebdb7b1f3ced3a7c4685d72645b2b6c +size 17324 diff --git a/figures/tag-definition.tex b/figures/tag-definition.tex new file mode 100644 index 0000000..b3a8e30 --- /dev/null +++ b/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} diff --git a/report.org b/report.org index 4adb03f..7f03b27 100644 --- a/report.org +++ b/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. diff --git a/report.pdf b/report.pdf index 7552402..9bd59a3 100644 --- a/report.pdf +++ b/report.pdf @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:41c973b38fc6b33997e77ad1d255ab6e35cf5f58574edd27da34a5158a294e34 -size 154858 +oid sha256:3a208138c7b9af707945b5659f0df46d116885bf91721c7317ce1805e7777c5f +size 180911