% This file was produced by plot-vcfstats, the command line was:
%   plot-vcfstats --title freebayes.BC2.v4 --prefix freebayes.BC2.v4.plot freebayes.BC2.v4.vcf.stats
%
% Edit as necessary and recreate the PDF by running
%   pdflatex summary.tex
%

% Slides style and dimensions
%
\nonstopmode
\documentclass[17pt]{memoir}
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\setlength{\parskip}{0pt}
\setheaderspaces{*}{1mm}{*}
\setmarginnotes{1mm}{1mm}{1mm}
\checkandfixthelayout[fixed]
\usepackage{charter}   % font
\pagestyle{plain}
\makeevenfoot{plain}{}{}{\thepage}
\makeoddfoot{plain}{}{}{\thepage}
\usepackage{graphicx}

% For colored tables. If xcolor.sty is not available on your system,
% download xcolor.sty.gz LaTeX class style from
%   http://www.ukern.de/tex/xcolor.html
% Unpack and install system-wide or place elsewhere and make available by
% setting the TEXINPUTS environment variable (note the colon)
%   export TEXINPUTS=some/dir:
% The list of the recognised path can be obtained by running `kpsepath tex`
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\usepackage{multirow}
\setlength{\tabcolsep}{0.6em}
\renewcommand{\arraystretch}{1.2}
        
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\definecolor{row2}{rgb}{1,0.92,0.8}    % #FFEBCC
\setlength{\arrayrulewidth}{1.5pt}

% Slide headings
\newcommand*{\head}[1]{{\Large\centerline{#1}\vskip0.5em}}

% Slide definition
\newcommand*{\hslide}[2]{%
        \head{#1}%
        \begin{vplace}[0.5]\centerline{#2}\end{vplace}\newpage}
\newcommand{\pdf}[2]{\IfFileExists{#2}{\includegraphics[#1]{#2}}{}}


% The actual slides
\begin{document}
        
% Table with summary numbers
%
\hslide{Summary Numbers}{
\begin{minipage}{\textwidth}\centering
\small \rowcolors*{3}{row2}{row1} \arrayrulecolor{black}
\begin{tabular}{l | r r r | r r | r | r}
\multicolumn{1}{>{\columncolor{hcol1}}l|}{}
& \multicolumn{3}{>{\columncolor{hcol1}}c|}{SNPs}
& \multicolumn{2}{>{\columncolor{hcol1}}c|}{indels}
& \multicolumn{1}{>{\columncolor{hcol1}}c|}{MNPs}
& \multicolumn{1}{>{\columncolor{hcol1}}c}{others}  \\
%
\multicolumn{1}{>{\columncolor{hcol2}}l|}{Callset}
& \multicolumn{1}{>{\columncolor{hcol2}}c}{n}
& \multicolumn{1}{>{\columncolor{hcol2}}c }{ts/tv}
& \multicolumn{1}{>{\columncolor{hcol2}}c|}{\footnotesize(1st ALT)}
& \multicolumn{1}{>{\columncolor{hcol2}}c}{n}
& \multicolumn{1}{>{\columncolor{hcol2}}c}{frm$^*$}
& \multicolumn{1}{>{\columncolor{hcol2}}c|}{}
& \multicolumn{1}{>{\columncolor{hcol2}}c}{} \\ \hline
         freebayes.BC2.v4 & 192,718 & 1.61 & 1.62 & 11,092 & -- & 35,218 & 6,130 \\ 
%
        \multicolumn{8}{r}{$^*$ frameshift ratio: out/(out+in)} \\
        \end{tabular}
        \\ \vspace{1em}
        \begin{tabular}{l | r r r | r r}
        \multicolumn{1}{>{\columncolor{hcol1}}l|}{}
        & \multicolumn{3}{>{\columncolor{hcol1}}c|}{singletons {\footnotesize(AC=1)}}
        & \multicolumn{2}{>{\columncolor{hcol1}}c}{multiallelic}  \\
        %
        \multicolumn{1}{>{\columncolor{hcol2}}l|}{Callset}
        & \multicolumn{1}{>{\columncolor{hcol2}}c}{SNPs}
        & \multicolumn{1}{>{\columncolor{hcol2}}c}{ts/tv}
        & \multicolumn{1}{>{\columncolor{hcol2}}c}{indels}
        & \multicolumn{1}{>{\columncolor{hcol2}}c}{sites}
        & \multicolumn{1}{>{\columncolor{hcol2}}c}{SNPs} \\ \hline
     freebayes.BC2.v4 & 2.2\% & 1.35 & 0.8\% & 10,761 &1,196 \\ 
 \end{tabular}
\vspace{2em}
\begin{itemize}[-]
\setlength{\itemsep}{0pt}
        \item freebayes.BC2.v4 .. \texttt{\footnotesize freebayes.BC2.v4.reordered.vcf.gz}
\end{itemize}\end{minipage}}

        
% Ts/Tv stratified by QUAL
%
\hslide{Ts/Tv stratified by QUAL}{\includegraphics[width=15cm]{{tstv_by_qual.0}.png}}
        
% Indel distribution
%
\hslide{Indel distribution}{\includegraphics[width=15cm]{{indels.0}.png}}
        
% Depth distribution
%
\hslide{Depth distribution}{\includegraphics[width=15cm]{{depth.0}.png}}
        
% Substitution types
%
\hslide{Substitution types}{\includegraphics[width=15cm]{{substitutions.0}.png}}
        
\end{document}