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index.tex
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\title{A Guide to Interpreting the Results of MetaDAG Analysis}
\author{}
\date{}
\begin{document}
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\chapter{Introduction}\label{introduction}
As an illustrative example for interpreting
\href{https://bioinfo.uib.es/metadag/}{metaDAG} results, we consider
here the Eukaryotes test presented in Section 2.5. Namely, we consider
all Eukaryotes from the KEGG database.
\href{https://www.github.com/biocom-uib/metadag}{Experiment github.}
First of all, results must be downloaded from:
Hash:
\href{https://bioinfo.uib.es/metadag/handleExperiment/0a845f74-826e-3b46-aed9-e7ecf74db262}{0a845f74-826e-3b46-aed9-e7ecf74db262}
URL:
(https://bioinfo.uib.es/metadag/handleExperiment/result\_0a845f74-826e-3b46-aed9-e7ecf74db262)
and saved in the folder:
``data/0a845f74-826e-3b46-aed9-e7ecf74db262''.
\begin{Shaded}
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\FunctionTok{library}\NormalTok{(tidyverse)}
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\FunctionTok{library}\NormalTok{(factoextra)}
\FunctionTok{library}\NormalTok{(RColorBrewer)}
\FunctionTok{library}\NormalTok{(kableExtra)}
\FunctionTok{library}\NormalTok{(igraph)}
\FunctionTok{library}\NormalTok{(GGally)}
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\includegraphics[width=1\textwidth,height=\textheight]{figures/screen_2.png}
\includegraphics[width=1\textwidth,height=\textheight]{figures/screen_3.png}
\includegraphics[width=1\textwidth,height=\textheight]{figures/screen_4.png}
\bookmarksetup{startatroot}
\chapter{Load data}\label{load-data}
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\toprule\noalign{}
Directory\_files\_and\_folders & Type \\
\midrule\noalign{}
\endhead
\bottomrule\noalign{}
\endlastfoot
Different\_MBB.csv & Data file \\
Different\_mDAG.csv & Data file \\
Global & Directory \\
Groups & Directory \\
Individuals & Directory \\
Report.pdf & Data file \\
Results.csv & Data file \\
Similarities\_MBB\_MSAMethod.csv & Data file \\
Similarities\_MBB\_MunkresMethod.csv & Data file \\
Similarities\_mDAG\_MSAMethod.csv & Data file \\
Similarities\_mDAG\_MunkresMethod.csv & Data file \\
TaxonomyLevels & Directory \\
\end{longtable}
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\section{Load metadata}\label{load-metadata}
Organisms are sorted by Kingdom, Phylum and Class:
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[1] "data/0a845f74-826e-3b46-aed9-e7ecf74db262/"
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\FunctionTok{rm}\NormalTok{(taxo)}
\NormalTok{aux}\OtherTok{=}\FunctionTok{table}\NormalTok{(meta\_taxo}\SpecialCharTok{$}\NormalTok{Kingdom)}
\NormalTok{Freq\_Kingdom}\OtherTok{=}\FunctionTok{tibble}\NormalTok{(}\AttributeTok{Kingdom=}\FunctionTok{names}\NormalTok{(aux),}\AttributeTok{Freq\_Kingdom=}\NormalTok{aux)}
\NormalTok{aux}\OtherTok{=}\FunctionTok{table}\NormalTok{(meta\_taxo}\SpecialCharTok{$}\NormalTok{Phylum)}
\NormalTok{Freq\_Phylum}\OtherTok{=}\FunctionTok{tibble}\NormalTok{(}\AttributeTok{Phylum=}\FunctionTok{names}\NormalTok{(aux),}\AttributeTok{Freq\_Phylum=}\NormalTok{aux)}
\NormalTok{aux}\OtherTok{=}\FunctionTok{table}\NormalTok{(meta\_taxo}\SpecialCharTok{$}\NormalTok{Class)}
\NormalTok{Freq\_Class}\OtherTok{=}\FunctionTok{tibble}\NormalTok{(}\AttributeTok{Class=}\FunctionTok{names}\NormalTok{(aux),}\AttributeTok{Freq\_Class=}\NormalTok{aux)}
\NormalTok{meta\_taxo }\OtherTok{=}\NormalTok{ meta\_taxo }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{left\_join}\NormalTok{(Freq\_Kingdom) }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{left\_join}\NormalTok{(Freq\_Phylum) }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{left\_join}\NormalTok{(Freq\_Class)}
\NormalTok{meta\_taxo }\OtherTok{=}\NormalTok{ meta\_taxo }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{arrange}\NormalTok{(}\FunctionTok{desc}\NormalTok{(Freq\_Kingdom),}
\FunctionTok{desc}\NormalTok{(Freq\_Phylum),}
\FunctionTok{desc}\NormalTok{(Freq\_Class))}
\CommentTok{\#arrange metaxto by frequencies of kingom phylum and class}
\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{kable}\NormalTok{(}\FunctionTok{head}\NormalTok{(meta\_taxo))}
\end{Highlighting}
\end{Shaded}
\begin{longtable}[]{@{}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0643}}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0571}}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0857}}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0571}}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0714}}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0571}}
>{\raggedright\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.3500}}
>{\raggedleft\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0929}}
>{\raggedleft\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0857}}
>{\raggedleft\arraybackslash}p{(\columnwidth - 18\tabcolsep) * \real{0.0786}}@{}}
\toprule\noalign{}
\begin{minipage}[b]{\linewidth}\raggedright
Organism
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
Kingdom
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
Phylum
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
Class
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
Groups
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
mDAG\_Id
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
Full\_Name
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedleft
Freq\_Kingdom
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedleft
Freq\_Phylum
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedleft
Freq\_Class
\end{minipage} \\
\midrule\noalign{}
\endhead
\bottomrule\noalign{}
\endlastfoot
aamp & Animals & Vertebrates & Mammals & Cluster 1 & 0313 & Arvicola
amphibius (Eurasian water vole) & 535 & 331 & 139 \\
afz & Animals & Vertebrates & Mammals & Cluster 1 & 0143 & Antechinus
flavipes (yellow-footed antechinus) & 535 & 331 & 139 \\
ajm & Animals & Vertebrates & Mammals & Cluster 1 & 0221 & Artibeus
jamaicensis (Jamaican fruit-eating bat) & 535 & 331 & 139 \\
aju & Animals & Vertebrates & Mammals & Cluster 1 & 0224 & Acinonyx
jubatus (cheetah) & 535 & 331 & 139 \\
aml & Animals & Vertebrates & Mammals & Cluster 1 & 0279 & Ailuropoda
melanoleuca (giant panda) & 535 & 331 & 139 \\
anu & Animals & Vertebrates & Mammals & Cluster 1 & 0310 & Arvicanthis
niloticus (African grass rat) & 535 & 331 & 139 \\
\end{longtable}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{table}\NormalTok{(meta\_taxo}\SpecialCharTok{$}\NormalTok{Kingdom) }\SpecialCharTok{\%\textgreater{}\%}\NormalTok{ kable }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{kable\_styling}\NormalTok{(}\StringTok{"striped"}\NormalTok{, }\AttributeTok{full\_width =}\NormalTok{ F,}\AttributeTok{position=}\StringTok{"left"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{scroll\_box}\NormalTok{(}\AttributeTok{width =} \StringTok{"400px"}\NormalTok{, }\AttributeTok{height =} \StringTok{"200px"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable*}[l]{lr}
\toprule
Var1 & Freq\\
\midrule
Animals & 535\\
Fungi & 154\\
Plants & 139\\
Protists & 56\\
\bottomrule
\end{longtable*}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{table}\NormalTok{(meta\_taxo}\SpecialCharTok{$}\NormalTok{Phylum,meta\_taxo}\SpecialCharTok{$}\NormalTok{Kingdom) }\SpecialCharTok{\%\textgreater{}\%}\NormalTok{ kable }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{kable\_styling}\NormalTok{(}\StringTok{"striped"}\NormalTok{, }\AttributeTok{full\_width =}\NormalTok{ F,}\AttributeTok{position=}\StringTok{"left"}\NormalTok{)}\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{scroll\_box}\NormalTok{(}\AttributeTok{width =} \StringTok{"500px"}\NormalTok{, }\AttributeTok{height =} \StringTok{"500px"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable*}[l]{lrrrr}
\toprule
& Animals & Fungi & Plants & Protists\\
\midrule
Alveolates & 0 & 0 & 0 & 25\\
Amoebozoa & 0 & 0 & 0 & 7\\
Annelids & 1 & 0 & 0 & 0\\
Arthropods & 158 & 0 & 0 & 0\\
Ascomycetes & 0 & 113 & 0 & 0\\
\addlinespace
Basal & 0 & 0 & 2 & 0\\
Basidiomycetes & 0 & 36 & 0 & 0\\
Brachiopodas & 1 & 0 & 0 & 0\\
Cephalochordates & 2 & 0 & 0 & 0\\
Choanoflagellates & 0 & 0 & 0 & 2\\
\addlinespace
Cnidarians & 10 & 0 & 0 & 0\\
Cryptomonads & 0 & 0 & 0 & 1\\
Echinoderms & 3 & 0 & 0 & 0\\
Eudicots & 0 & 0 & 98 & 0\\
Euglenozoa & 0 & 0 & 0 & 9\\
\addlinespace
Ferns & 0 & 0 & 1 & 0\\
Flatworms & 4 & 0 & 0 & 0\\
Green & 0 & 0 & 11 & 0\\
Haptophyta & 0 & 0 & 0 & 1\\
Hemichordates & 1 & 0 & 0 & 0\\
\addlinespace
Heterolobosea & 0 & 0 & 0 & 1\\
Metamonada & 0 & 0 & 0 & 2\\
Microsporidians & 0 & 5 & 0 & 0\\
Mollusks & 14 & 0 & 0 & 0\\
Monocots & 0 & 0 & 23 & 0\\
\addlinespace
Mosses & 0 & 0 & 1 & 0\\
Nematodes & 6 & 0 & 0 & 0\\
Placozoans & 1 & 0 & 0 & 0\\
Poriferans & 1 & 0 & 0 & 0\\
Red & 0 & 0 & 3 & 0\\
\addlinespace
Stramenopiles & 0 & 0 & 0 & 8\\
Tunicates & 2 & 0 & 0 & 0\\
Vertebrates & 331 & 0 & 0 & 0\\
\bottomrule
\end{longtable*}
\section{Table of MBBs}\label{table-of-mbbs}
In this example \texttt{MBB} is a table with 5149 rows and 4122 columns.
It displays, for every MBB, the selected groups (Kingdoms, families,
etc.) to which it belongs.
\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\#100}
\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{kable}\NormalTok{(MBB[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{20}\NormalTok{,}\DecValTok{1}\SpecialCharTok{:}\DecValTok{10}\NormalTok{]) }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{scroll\_box}\NormalTok{(}\AttributeTok{width =} \StringTok{"100\%"}\NormalTok{, }\AttributeTok{height =} \StringTok{"200px"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable*}[t]{lrrrrrrrrr}
\toprule
MBB Id & natural & \#pathways & Protists & Fungi & Plants & Animals & Alveolates & Amoebozoa & Annelids\\
\midrule
0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0.0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0.0.0 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.0.0.0 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
\addlinespace
0.0.0.0.0.0 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.0.1 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.0.2 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.1 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0.1.0 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 1\\
\addlinespace
0.0.1.1 & 1 & 1 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0.1.1.0 & 1 & 1 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0.1.2 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.1.3 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.1.4 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
\addlinespace
0.0.1.4.0 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.1.4.0.0 & 1 & 1 & 0 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.1.5 & 1 & 1 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0.0.1.6 & 1 & 4 & 3 & 0 & 0 & 1 & 0 & 0 & 0\\
0.0.1.6.0 & 1 & 3 & 0 & 0 & 3 & 0 & 0 & 0 & 0\\
\bottomrule
\end{longtable*}
\section{Table of m-DAGs}\label{table-of-m-dags}
In this example \texttt{mDAG} is a table with 1132 rows and 5278
columns. It displays, for every m-DAG, the selected groups (Kingdoms,
families, etc.) in which it belongs.
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{kable}\NormalTok{(mDAG[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{20}\NormalTok{,}\DecValTok{1}\SpecialCharTok{:}\DecValTok{10}\NormalTok{]) }\SpecialCharTok{\%\textgreater{}\%} \FunctionTok{scroll\_box}\NormalTok{(}\AttributeTok{width =} \StringTok{"100\%"}\NormalTok{, }\AttributeTok{height =} \StringTok{"200px"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable*}[t]{lrrrrrrrrr}
\toprule
mDAG Id & \#Categories & Animals & Plants & Fungi & Protists & Alveolates & Amoebozoa & Annelids & Arthropods\\
\midrule
0001 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0002 & 2 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0\\
0003 & 2 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0004 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0005 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
\addlinespace
0006 & 3 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0007 & 2 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0008 & 3 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0009 & 3 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0\\
0010 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
\addlinespace
0011 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0012 & 3 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0\\
0013 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0014 & 3 & 0 & 0 & 0 & 1 & 1 & 0 & 0 & 0\\
0015 & 2 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0\\
\addlinespace
0016 & 3 & 0 & 0 & 0 & 1 & 0 & 1 & 0 & 0\\
0017 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0018 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
0019 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 1\\
0020 & 3 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0\\
\bottomrule
\end{longtable*}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{dim}\NormalTok{(mDAG)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] 1132 5278
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(mDAG)[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{6}\NormalTok{]}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "mDAG Id" "#Categories" "Animals" "Plants" "Fungi"
[6] "Protists"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{head}\NormalTok{(}\FunctionTok{names}\NormalTok{(mDAG)[}\DecValTok{7}\SpecialCharTok{:}\NormalTok{(}\FunctionTok{dim}\NormalTok{(mDAG)[}\DecValTok{2}\NormalTok{]}\SpecialCharTok{{-}}\DecValTok{1150}\NormalTok{)])}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "Alveolates" "Amoebozoa" "Annelids"
[4] "Arthropods" "Ascomycetes" "Basal angiosperms"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\# 28 to 1213 code MBB: 1 if MBB in mDAG 0}
\end{Highlighting}
\end{Shaded}
\section{Results Table}\label{results-table}
The \texttt{Results} table contains for every organism (row) the
following information: its category (taxonomy), selected group, Full
name, m-DAG id and all reactions name id with their corresponding
enzyme. When a reaction is present in the corresponding m-DAG, the MBB
to which it belongs is displayed in this column.
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{kable}\NormalTok{(Results[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{20}\NormalTok{,}\DecValTok{1}\SpecialCharTok{:}\DecValTok{10}\NormalTok{])}\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{row\_spec}\NormalTok{(}\DecValTok{0}\NormalTok{, }\AttributeTok{angle =} \DecValTok{0}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{scroll\_box}\NormalTok{(}\AttributeTok{width =} \StringTok{"300\%"}\NormalTok{, }\AttributeTok{height =} \StringTok{"1000px"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable*}[t]{llllllrlll}
\toprule
\rotatebox{0}{Organism} & \rotatebox{0}{Categories} & \rotatebox{0}{Groups} & \rotatebox{0}{mDAG\_Id} & \rotatebox{0}{Full\_Name} & \rotatebox{0}{R00005(3.5.1.54)} & \rotatebox{0}{R00009(1.11.1.6)} & \rotatebox{0}{R00010(3.2.1.28)} & \rotatebox{0}{R00014(1.2.4.1)} & \rotatebox{0}{R00014(4.1.1.1)}\\
\midrule
aaf & Protists\&\#124;Stramenopiles\&\#124;Pelagophytes & MSA Cluster 3\&\#124;MUN Cluster 3 & 0036 & Aureococcus anophagefferens & NA & NA & 0.0.10.0.15 & 0.0.10.0.15 & NA\\
aag & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0035 & Aedes aegypti (yellow fever mosquito) & NA & 3936 & 0.9.27.7.36.14 & 0.9.27.7.36.14 & NA\\
aalb & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0276 & Aedes albopictus (Asian tiger mosquito) & NA & 3936 & 0.9.27.7.36.18 & 0.9.27.7.36.18 & NA\\
aali & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0267 & Anopheles albimanus & NA & 3936 & 0.9.27.7.36.65 & 0.9.27.7.36.65 & NA\\
aalt & Fungi\&\#124;Ascomycetes\&\#124;Dothideomycetes & Fungui and Algae\&\#124;MSA Cluster 3\&\#124;MSA Fungui and Nematodes and Flatworms\&\#124;MUN Cluster 3\&\#124;MUN Fungui and Nematodes and Flatworms & 0240 & Alternaria alternata & NA & 3936 & 0.0.9.20.0.5.6.7 & 0.0.9.20.0.5.6.7 & 0.0.9.20.0.5.6.7\\
\addlinespace
aam & Animals\&\#124;Vertebrates\&\#124;Birds & Cluster 1 & 0040 & Apteryx mantelli mantelli (North Island brown kiwi) & NA & 3936 & NA & 0.9.26.15.46 & NA\\
aamp & Animals\&\#124;Vertebrates\&\#124;Mammals & Cluster 1 & 0313 & Arvicola amphibius (Eurasian water vole) & NA & 3936 & 0.0.9.20.0.6.0.39 & 0.9.26.18.2.0 & NA\\
aang & Animals\&\#124;Vertebrates\&\#124;Fishes & Cluster 1 & 0317 & Anguilla anguilla (European eel) & NA & 3936 & 0.0.9.20.0.6.0.39 & 0.9.26.17.0.0 & NA\\
aara & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0362 & Anopheles arabiensis & NA & 3936 & 0.9.27.7.36.34 & 0.9.27.7.36.34 & NA\\
abe & Fungi\&\#124;Ascomycetes\&\#124;Eurotiomycetes & Fungui and Algae\&\#124;MSA Cluster 3\&\#124;MSA Fungui and Nematodes and Flatworms\&\#124;MUN Cluster 3\&\#124;MUN Fungui and Nematodes and Flatworms & 0060 & Trichophyton benhamiae & NA & 3936 & 0.0.9.20.0.5.7.0 & 0.0.9.20.0.5.7.0 & 0.0.9.20.0.5.7.0\\
\addlinespace
abp & Fungi\&\#124;Basidiomycetes & Fungui and Algae\&\#124;MSA Cluster 3\&\#124;MSA Fungui and Nematodes and Flatworms\&\#124;MUN Cluster 3\&\#124;MUN Fungui and Nematodes and Flatworms & 0068 & Agaricus bisporus var. burnettii JB137-S8 & NA & 3936 & 0.0.9.20.0.6.1 & 0.0.9.20.0.6.1 & 0.0.9.20.0.6.1\\
abv & Fungi\&\#124;Basidiomycetes & Fungui and Algae\&\#124;MSA Cluster 3\&\#124;MSA Fungui and Nematodes and Flatworms\&\#124;MUN Cluster 3\&\#124;MUN Fungui and Nematodes and Flatworms & 0073 & Agaricus bisporus var. bisporus H97 & NA & 3936 & 0.0.9.20.0.6.3 & 0.0.9.20.0.6.3 & 0.0.9.20.0.6.3\\
acan & Protists\&\#124;Amoebozoa\&\#124;Acanthamoeba & MSA Cluster 3\&\#124;MUN Cluster 3 & 0873 & Acanthamoeba castellanii & NA & 3936 & NA & 0.0.10.0.3 & NA\\
acar & Animals\&\#124;Vertebrates\&\#124;Birds & Cluster 1 & 0884 & Antrostomus carolinensis (chuck-will's-widow) & NA & 3936 & NA & 0.9.26.15.59 & NA\\
acep & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0054 & Atta cephalotes (leaf cutting ant) & NA & 3936 & 0.9.27.7.36.56 & 0.9.27.7.36.56 & NA\\
\addlinespace
acer & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0057 & Apis cerana (Asiatic honeybee) & NA & 3936 & 0.9.27.7.35.34 & 0.9.27.7.35.34 & NA\\
achc & Animals\&\#124;Vertebrates\&\#124;Birds & Cluster 1 & 0103 & Aquila chrysaetos chrysaetos (golden eagle) & NA & 3936 & NA & 0.9.26.15.2.0 & NA\\
ache & Fungi\&\#124;Ascomycetes\&\#124;Eurotiomycetes & Fungui and Algae\&\#124;MSA Cluster 3\&\#124;MSA Fungui and Nematodes and Flatworms\&\#124;MUN Cluster 3\&\#124;MUN Fungui and Nematodes and Flatworms & 0106 & Aspergillus chevalieri & NA & 3936 & 0.0.9.20.0.5.7.2 & 0.0.9.20.0.5.7.2 & 0.0.9.20.0.5.7.2\\
achl & Animals\&\#124;Vertebrates\&\#124;Birds & Cluster 1 & 0081 & Acanthisitta chloris (rifleman) & NA & 3936 & NA & 0.9.26.15.1.1.0.0 & NA\\
acoz & Animals\&\#124;Arthropods\&\#124;Insects & MSA Cluster 2\&\#124;MUN Cluster 2 & 0255 & Anopheles coluzzii & NA & 3936 & 0.9.27.7.36.22 & 0.9.27.7.36.22 & NA\\
\bottomrule
\end{longtable*}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{dim}\NormalTok{(Results)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] 1132 3998
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(Results)[}\DecValTok{1}\NormalTok{]}\CommentTok{\# organisms kegg id class representant of mDAG}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "Organism"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(Results)[}\DecValTok{2}\NormalTok{]}\CommentTok{\# taxonomy separate by |}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "Categories"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(Results)[}\DecValTok{3}\NormalTok{]}\CommentTok{\# groups }
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "Groups"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(Results)[}\DecValTok{4}\NormalTok{]}\CommentTok{\# mDAG\_Id }
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "mDAG_Id"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(Results)[}\DecValTok{5}\NormalTok{]}\CommentTok{\# Full name representant}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "Full_Name"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{names}\NormalTok{(Results)[}\DecValTok{6}\SpecialCharTok{:}\DecValTok{36}\NormalTok{]}\CommentTok{\# columns 6 to 3998 }
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "R00005(3.5.1.54)" "R00009(1.11.1.6)" "R00010(3.2.1.28)"
[4] "R00014(1.2.4.1)" "R00014(4.1.1.1)" "R00021(1.4.7.1)"
[7] "R00022(3.2.1.52)" "R00024(4.1.1.39)" "R00028(3.2.1.20)"
[10] "R00031(1.10.3.1)" "R00032(1.13.11.63)" "R00036(4.2.1.24)"
[13] "R00045(1.10.3.1)" "R00066(2.5.1.9)" "R00068(1.10.3.3)"
[16] "R00073(1.14.99.1)" "R00075(2.5.1.43)" "R00078(1.16.3.1)"
[19] "R00084(2.5.1.61)" "R00086(3.6.1.15)" "R00086(3.6.1.5)"
[22] "R00087(3.6.1.9)" "R00093(1.4.1.14)" "R00095(1.6.5.4)"
[25] "R00100(1.6.2.2)" "R00102(3.2.2.5)" "R00102(3.2.2.6)"
[28] "R00103(3.6.1.22)" "R00103(3.6.1.9)" "R00104(2.7.1.23)"
[31] "R00111(1.14.13.39)"
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\# reactions name id with its enzyme.}
\end{Highlighting}
\end{Shaded}
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{reactions}\OtherTok{=}\FunctionTok{names}\NormalTok{(Results)[}\SpecialCharTok{{-}}\FunctionTok{c}\NormalTok{(}\DecValTok{1}\SpecialCharTok{:}\DecValTok{5}\NormalTok{)]}
\NormalTok{reverse\_reactions}\OtherTok{=}\NormalTok{stringr}\SpecialCharTok{::}\FunctionTok{str\_detect}\NormalTok{(reactions,}\StringTok{"rev"}\NormalTok{)}
\NormalTok{reverse\_reactions}\OtherTok{=}\FunctionTok{table}\NormalTok{(reverse\_reactions)}
\FunctionTok{dimnames}\NormalTok{(reverse\_reactions)}\SpecialCharTok{$}\NormalTok{reverse\_reactions}\OtherTok{=}
\FunctionTok{c}\NormalTok{(}\StringTok{"Non reverse reaction"}\NormalTok{,}\StringTok{"Reverse reaction"}\NormalTok{)}
\NormalTok{reverse\_reactions }\SpecialCharTok{\%\textgreater{}\%}\NormalTok{ kable }\SpecialCharTok{\%\textgreater{}\%}
\FunctionTok{kable\_styling}\NormalTok{(}\StringTok{"striped"}\NormalTok{, }\AttributeTok{full\_width =}\NormalTok{ F,}\AttributeTok{position=}\StringTok{"left"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}
\begin{longtable*}[l]{lr}
\toprule
reverse\_reactions & Freq\\
\midrule
Non reverse reaction & 3399\\
Reverse reaction & 594\\
\bottomrule
\end{longtable*}
\bookmarksetup{startatroot}
\chapter{Metabolic Graphs}\label{metabolic-graphs}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{gc}\NormalTok{()}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 2771214 148.0 4247817 226.9 4247817 226.9
Vcells 4571320 34.9 10146329 77.5 8012275 61.2
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{load}\NormalTok{(}\AttributeTok{file=}\StringTok{\textquotesingle{}metadag\_work\_space.RData\textquotesingle{}}\NormalTok{)}
\FunctionTok{gc}\NormalTok{()}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 2870799 153.4 4247817 226.9 4247817 226.9
Vcells 38153618 291.1 49085484 374.5 38174318 291.3
\end{verbatim}
We present here some analysis examples of the metabolic graphs generated
in GraphML format.
\section{Metabolic graphs for each
organism}\label{metabolic-graphs-for-each-organism}
Read the individual metabolic graphs generated for Homo sapiens (KEGG
id: hsa) in the directory(Individuals/hsa)
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{experiment}\OtherTok{=}
\StringTok{"0a845f74{-}826e{-}3b46{-}aed9{-}e7ecf74db262/"}
\NormalTok{path\_exp}\OtherTok{=}\FunctionTok{paste0}\NormalTok{(}\StringTok{"data/"}\NormalTok{,experiment)}
\NormalTok{files\_hsa}\OtherTok{=}\FunctionTok{dir}\NormalTok{(}\FunctionTok{paste0}\NormalTok{(path\_exp,}\StringTok{"Individuals/hsa"}\NormalTok{))}
\NormalTok{files\_hsa}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "hsa_mDAG.graphml" "hsa_mDAG.pdf" "hsa_mDAG.svg"
[4] "hsa_mDAG_adj.csv" "hsa_mDAG_biggerDAG.pdf" "hsa_mDAG_biggerDAG.svg"
[7] "hsa_mDAG_nl.csv" "hsa_mDAG_structure.csv" "hsa_R_adj.csv"
[10] "hsa_R_nl.csv" "hsa_RC.graphml" "hsa_RC.pdf"
[13] "hsa_RC.svg" "hsa_summary.txt"
\end{verbatim}
\begin{longtable}[]{@{}
>{\raggedright\arraybackslash}p{(\columnwidth - 2\tabcolsep) * \real{0.2190}}
>{\raggedright\arraybackslash}p{(\columnwidth - 2\tabcolsep) * \real{0.7810}}@{}}
\toprule\noalign{}
\begin{minipage}[b]{\linewidth}\raggedright
files\_Individual\_hsa
\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
Description
\end{minipage} \\
\midrule\noalign{}
\endhead
\bottomrule\noalign{}
\endlastfoot
hsa\_mDAG.graphml & m-DAG GraphML format \\
hsa\_mDAG.pdf & m-DAG pdf graphic \\
hsa\_mDAG.svg & m-DAG svg graphic \\
hsa\_mDAG\_adj.csv & csv file with the adjacency matrix of the m-DAG \\
hsa\_mDAG\_biggerDAG.pdf & pdf graphic with the biggest conected
componet of the m-DAG \\
hsa\_mDAG\_biggerDAG.svg & svg graphic with the biggest conected
componet of the m-DAG \\
hsa\_mDAG\_nl.csv & csv file with the node (MBBs) labels of the m-DAG \\
hsa\_mDAG\_structure.csv & csv file with all connected components of the
m-DAG \\
hsa\_R\_adj.csv & csv file with the adjacency matrix of the reaction
graph \\
hsa\_R\_nl.csv & csv file with the node (reactions) labels of the
reaction graph \\
hsa\_RC.graphml & reaction graph GraphML format \\
hsa\_RC.pdf & reaction graph pdf graphic \\
hsa\_RC.svg & reaction graph svg graphic \\
hsa\_summary.txt & text summary file with the number of MBBs, reactions,
etc. in the previous graphs \\
\end{longtable}
\section{Pan \& core metabolic graphs}\label{pan-core-metabolic-graphs}
Pan and core metabolic graphs for every group were generated. For
instance, one can read the pan and core metabolic graphs generated for
the group Algae in the directory (Groups/Algae).
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{files\_Algae}\OtherTok{=}\FunctionTok{dir}\NormalTok{(}\FunctionTok{paste0}\NormalTok{(path\_exp,}\StringTok{"Groups/Algae"}\NormalTok{))}
\NormalTok{files\_Algae}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
[1] "core" "pan"
\end{verbatim}
The global core reaction graph, which is the core of all the organisms'
reaction graphs in this Eukaryotes test, is empty.
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{graph\_core\_RC}\OtherTok{=}\FunctionTok{read.graph}\NormalTok{(}
\FunctionTok{paste0}\NormalTok{(path\_exp,}
\StringTok{"Global/core/core\_RC.graphml"}\NormalTok{),}
\AttributeTok{format =} \StringTok{"graphml"}\NormalTok{)}
\FunctionTok{summary}\NormalTok{(graph\_core\_RC)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
IGRAPH 1cff44a D--- 0 0 --
+ attr: color (v/c), label (v/c), id (v/c)
\end{verbatim}
The global core reaction graph has 0 vertex and 0 edges. It is an empty
graph.
The core reaction graph for the Algae group is:
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{include\_graphics}\NormalTok{(}
\FunctionTok{paste0}\NormalTok{(path\_exp,}\StringTok{"Groups/MSA\_Cluster\_3/core/MSA\_Cluster\_3\_core\_RC.pdf"}\NormalTok{))}
\end{Highlighting}
\end{Shaded}
\begin{figure}[H]
{\centering \includegraphics[width=1\textwidth,height=\textheight]{data/0a845f74-826e-3b46-aed9-e7ecf74db262/Groups/MSA_Cluster_3/core/MSA_Cluster_3_core_RC.pdf}
}
\caption{Algae core reaction graph}
\end{figure}%
The global core m-DAG, i.e., the core of all organisms in this example
is empty.
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{graph\_core\_mDAG}\OtherTok{=}\FunctionTok{read.graph}\NormalTok{(}
\FunctionTok{paste0}\NormalTok{(path\_exp,}\StringTok{"Global/core/core\_mDAG.graphml"}\NormalTok{),}
\AttributeTok{format =} \StringTok{"graphml"}\NormalTok{)}
\FunctionTok{summary}\NormalTok{(graph\_core\_mDAG)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
IGRAPH 1d0231c D--- 0 0 --
+ attr: color (v/c), label (v/c), id (v/c)
\end{verbatim}
The global core m-DAG has 0 vertex and 0 edges. It is an empty graph.
The core metabolic DAG for the Algae group is:
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{include\_graphics}\NormalTok{(}\FunctionTok{paste0}\NormalTok{(path\_exp, }\StringTok{"Groups/Algae/core/Algae\_core\_mDAG.pdf"}\NormalTok{))}
\end{Highlighting}
\end{Shaded}
\begin{figure}[H]
{\centering \includegraphics[width=1\textwidth,height=\textheight]{data/0a845f74-826e-3b46-aed9-e7ecf74db262/Groups/Algae/core/Algae_core_mDAG.pdf}
}
\caption{Core m-DAG for Algae}
\end{figure}%
The global pan reaction graph for the Animals Kingdom is:
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{graph\_pan\_RC}\OtherTok{=}\FunctionTok{read.graph}\NormalTok{(}
\FunctionTok{paste0}\NormalTok{(path\_exp,}
\StringTok{"TaxonomyLevels/Kingdom/Animals/pan/Animals\_pan\_RC.graphml"}\NormalTok{),}
\AttributeTok{format =} \StringTok{"graphml"}\NormalTok{)}
\FunctionTok{summary}\NormalTok{(graph\_pan\_RC)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
IGRAPH 1d12675 D--- 4556 5798 --
+ attr: color (v/c), label (v/c), id (v/c), id (e/c)
\end{verbatim}
This pan reaction graph has 4556 nodes and 5798 edges.
\section{Graph's topology}\label{graphs-topology}
From the GraphML files, one can extract topological information. Some
examples are as follows.
The diagram below illustrates the distribution of node degrees for an
m-DAG.
\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{graph\_mDAG}\OtherTok{=}\FunctionTok{read.graph}\NormalTok{(}
\FunctionTok{paste0}\NormalTok{(path\_exp,}
\StringTok{"Individuals/hsa/hsa\_mDAG.graphml"}\NormalTok{),}
\AttributeTok{format=} \StringTok{"graphml"}\NormalTok{)}
\FunctionTok{summary}\NormalTok{(graph\_mDAG)}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
IGRAPH 1d14d00 D--- 1026 1086 --
+ attr: color (v/c), label (v/c), id (v/c), id (e/c)
\end{verbatim}
\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{barplot}\NormalTok{(}\FunctionTok{table}\NormalTok{(igraph}\SpecialCharTok{::}\FunctionTok{degree}\NormalTok{(graph\_mDAG,}\AttributeTok{mode=}\StringTok{"all"}\NormalTok{)),}
\AttributeTok{ylim=}\FunctionTok{c}\NormalTok{(}\DecValTok{0}\NormalTok{,}\DecValTok{350}\NormalTok{),}\AttributeTok{col=}\StringTok{"blue"}\NormalTok{,}
\AttributeTok{main=}\StringTok{"Frequency of Node Degrees"}\NormalTok{,}
\AttributeTok{ylab=}\StringTok{"Frequency"}\NormalTok{,}\AttributeTok{xlab=}\StringTok{"Degree"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}