Zarr-sgkit-figure

Zarr-sgkit-figure.tex

\documentclass{article}
\usepackage{forest}
\usepackage{tikz}
\usetikzlibrary{quotes,arrows.meta,3d}

\title{Zarr-sgkit}
\author{Tim Millar}
\date{December 2023}

%% flexible cuboid from
%% https://tex.stackexchange.com/questions/267982/tikz-easy-drawing-of-cuboids

\makeatletter
\def\tikz@lib@cuboid@get#1{\pgfkeysvalueof{/tikz/cuboid/#1}}

\def\tikz@lib@cuboid@setup{%
   \pgfmathsetlengthmacro{\vxx}%
      {\tikz@lib@cuboid@get{xscale}*cos(\tikz@lib@cuboid@get{xangle})*1cm}
   \pgfmathsetlengthmacro{\vxy}%
      {\tikz@lib@cuboid@get{xscale}*sin(\tikz@lib@cuboid@get{xangle})*1cm}
   \pgfmathsetlengthmacro{\vyx}%
      {\tikz@lib@cuboid@get{yscale}*cos(\tikz@lib@cuboid@get{yangle})*1cm}
   \pgfmathsetlengthmacro{\vyy}%
      {\tikz@lib@cuboid@get{yscale}*sin(\tikz@lib@cuboid@get{yangle})*1cm}
   \pgfmathsetlengthmacro{\vzx}%
      {\tikz@lib@cuboid@get{zscale}*cos(\tikz@lib@cuboid@get{zangle})*1cm}
   \pgfmathsetlengthmacro{\vzy}%
      {\tikz@lib@cuboid@get{zscale}*sin(\tikz@lib@cuboid@get{zangle})*1cm}
}

\def\tikz@lib@cuboid@draw#1--#2--#3\pgf@stop{%
    \begin{scope}[join=bevel,x={(\vxx,\vxy)},y={(\vyx,\vyy)},z={(\vzx,\vzy)}]
       % first fill the faces with global and individual style
       % then draw the grids
       \begin{scope}[canvas is yz plane at x=#1]
          \draw[cuboid/all faces,cuboid/edges,cuboid/right face] 
                (0,0) -- ++(#2,0) -- ++(0,-#3) -- ++(-#2,0) -- cycle;
          \draw[cuboid/all grids,cuboid/right grid] (0,0) grid (#2,-#3);
       \end{scope}
       \begin{scope}[canvas is xy plane at z=0]
          \draw[cuboid/all faces,cuboid/edges,cuboid/front face] 
                (0,0) -- ++(#1,0) --  ++(0,#2) -- ++(-#1,0) -- cycle;
          \draw[cuboid/all grids,cuboid/front grid] (0,0) grid (#1,#2);
       \end{scope}
       \begin{scope}[canvas is xz plane at y=#2]
          \draw[cuboid/all faces,cuboid/edges,cuboid/top face] 
                (0,0) -- ++(#1,0) --  ++(0,-#3) -- ++(-#1,0) -- cycle;
          \draw[cuboid/all grids,cuboid/top grid] (0,0) grid (#1,-#3);
       \end{scope}
       % now, draw the hidden edges
       \draw[cuboid/hidden edges] (0,#2,-#3) -- (0,0,-#3) -- (0,0,0) 
                (0,0,-#3) -- ++(#1,0,0);
       % finally, draw the visible edges 
       \begin{scope}[canvas is yz plane at x=#1]
          \draw[cuboid/all faces,cuboid/right face,cuboid/edges,fill opacity=0] 
                (0,0) -- ++(#2,0) -- ++(0,-#3) -- ++(-#2,0) -- cycle;
       \end{scope}
       \begin{scope}[canvas is xy plane at z=0]
          \draw[cuboid/all faces,cuboid/front face,cuboid/edges,fill opacity=0] 
                (0,0) -- ++(#1,0) --  ++(0,#2) -- ++(-#1,0) -- cycle;
       \end{scope}
       \begin{scope}[canvas is xz plane at y=#2]
          \draw[cuboid/all faces,cuboid/top face,cuboid/edges,fill opacity=0] 
                (0,0) -- ++(#1,0) --  ++(0,-#3) -- ++(-#1,0) -- cycle;
       \end{scope}
       % define the anchors: 8 vertices
       \path (0,#2,0) coordinate (-left top front)
                      coordinate (-left front top)
                      coordinate (-top left front)
                      coordinate (-top front left)
                      coordinate (-front top left)
                      coordinate (-front left top);
       \path (0,#2,-#3) coordinate (-left top rear)
                        coordinate (-left rear top)
                        coordinate (-top left rear)
                        coordinate (-top rear left)
                        coordinate (-rear top left)
                        coordinate (-rear left top);
       \path (0,0,-#3) coordinate (-left bottom rear)
                       coordinate (-left rear bottom)
                       coordinate (-bottom left rear)
                       coordinate (-bottom rear left)
                       coordinate (-rear bottom left)
                       coordinate (-rear left bottom);
       \path (0,0,0) coordinate (-left bottom front)
                     coordinate (-left front bottom)
                     coordinate (-bottom left front)
                     coordinate (-bottom front left)
                     coordinate (-front bottom left)
                     coordinate (-front left bottom);
       \path (#1,#2,0) coordinate (-right top front)
                       coordinate (-right front top)
                       coordinate (-top right front)
                       coordinate (-top front right)
                       coordinate (-front top right)
                       coordinate (-front right top);
       \path (#1,#2,-#3) coordinate (-right top rear)
                         coordinate (-right rear top)
                         coordinate (-top right rear)
                         coordinate (-top rear right)
                         coordinate (-rear top right)
                         coordinate (-rear right top);
       \path (#1,0,-#3) coordinate (-right bottom rear)
                        coordinate (-right rear bottom)
                        coordinate (-bottom right rear)
                        coordinate (-bottom rear right)
                        coordinate (-rear bottom right)
                        coordinate (-rear right bottom);
       \path (#1,0,0) coordinate (-right bottom front)
                      coordinate (-right front bottom)
                      coordinate (-bottom right front)
                      coordinate (-bottom front right)
                      coordinate (-front bottom right)
                      coordinate (-front right bottom);
       % centers of the 6 faces
       \coordinate (-left center) at (0,.5*#2,-.5*#3);
       \coordinate (-right center) at (#1,.5*#2,-.5*#3);
       \coordinate (-top center) at (.5*#1,#2,-.5*#3);
       \coordinate (-bottom center) at (.5*#1,0,-.5*#3);
       \coordinate (-front center) at (.5*#1,.5*#2,0);
       \coordinate (-rear center) at (.5*#1,.5*#2,-#3);
       % center of the cuboid
       \coordinate (-center) at (.5*#1,.5*#2,-.5*#3);
       % centers of the 12 edges
       \path (0,#2,-.5*#3) coordinate (-left top center) 
                           coordinate (-top left center);
       \path (.5*#1,#2,-#3) coordinate (-top rear center)
                            coordinate (-rear top center);
       \path (#1,#2,-.5*#3) coordinate (-right top center)
                            coordinate (-top right center);
       \path (.5*#1,#2,0) coordinate (-top front center)
                          coordinate (-front top center);
       \path (0,0,-.5*#3) coordinate (-left bottom center) 
                           coordinate (-bottom left center);
       \path (.5*#1,0,-#3) coordinate (-bottom rear center)
                            coordinate (-rear bottom center);
       \path (#1,0,-.5*#3) coordinate (-right bottom center)
                            coordinate (-bottom right center);
       \path (.5*#1,0,0) coordinate (-bottom front center)
                          coordinate (-front bottom center);
       \path (0,.5*#2,0) coordinate (-left front center) 
                           coordinate (-front left center);
       \path (0,.5*#2,-#3) coordinate (-left rear center)
                            coordinate (-rear left center);
       \path (#1,.5*#2,0) coordinate (-right front center)
                            coordinate (-front right center);
       \path (#1,.5*#2,-#3) coordinate (-right rear center)
                          coordinate (-rear right center);
    \end{scope}
}

\tikzset{
  pics/cuboid/.style = {
    setup code = \tikz@lib@cuboid@setup,
    background code = \tikz@lib@cuboid@draw#1\pgf@stop
  },
  pics/cuboid/.default={1--1--1},
  cuboid/.is family,
  cuboid,
  all faces/.style={fill=white},
  all grids/.style={draw=none},
  front face/.style={},
  front grid/.style={},
  right face/.style={},
  right grid/.style={},
  top face/.style={},
  top grid/.style={},
  edges/.style={},
  hidden edges/.style={draw=none},
  xangle/.initial=0,
  yangle/.initial=90,
  zangle/.initial=210,
  xscale/.initial=1,
  yscale/.initial=1,
  zscale/.initial=0.5
}

\newcommand{\tikzcuboidreset}{
\tikzset{cuboid,
  all faces/.style={fill=white},
  all grids/.style={draw=none},
  front face/.style={},
  front grid/.style={},
  right face/.style={},
  right grid/.style={},
  top face/.style={},
  top grid/.style={},
  edges/.style={},
  hidden edges/.style={draw=none},
  xangle=0,
  yangle=90,
  zangle=225,
  xscale=1,
  yscale=1,
  zscale=0.5
}
}

\newcommand{\tikzcuboidset}{\@ifstar\tikzcuboidset@star\tikzcuboidset@nostar} 
\newcommand{\tikzcuboidset@nostar}[1]{\tikzcuboidreset\tikzset{cuboid,#1}}
\newcommand{\tikzcuboidset@star}[1]{\tikzset{cuboid,#1}}
\makeatother


\begin{document}

\maketitle

\begin{tikzpicture}

 %% sample_id
  \node at (2.0,6.6,-.5) {\ttfamily \scriptsize sample\textunderscore id};
  % bounds
  \draw[densely dashed] (0,6.2,-.5) -- (3.9,6.2,-.5);
  \draw[densely dashed] (0,6.4,-.5) -- (3.9,6.4,-.5);
 \tikzcuboidset{front face/.style={fill=yellow!20},right face/.style={fill=green!10},top face/.style={fill=yellow!20}}
  \pic at (0,6.2,-.5) {cuboid=.9--.2--0};
  \pic at (1,6.2,-.5) {cuboid=.9--.2--0};
  \node at (2.5,6.3,-.5) {\ttfamily \dots};
  \pic at (3,6.2,-.5) {cuboid=.9--.2--0};

 %% sample_cohort
  \node at (2.0,5.9,-.5) {\ttfamily \scriptsize sample\textunderscore cohort};
  % bounds
  \draw[densely dashed] (0,5.5,-.5) -- (3.9,5.5,-.5);
  \draw[densely dashed] (0,5.7,-.5) -- (3.9,5.7,-.5);
 \tikzcuboidset{front face/.style={fill=yellow!20},right face/.style={fill=green!10},top face/.style={fill=yellow!20}}
  \pic at (0,5.5,-.5) {cuboid=.9--.2--0};
  \pic at (1,5.5,-.5) {cuboid=.9--.2--0};
  \node at (2.5,5.6,-.5) {\ttfamily \dots};
  \pic at (3,5.5,-.5) {cuboid=.9--.2--0};

 %% variant_contig
  \node[rotate=90] at (-1.5,2.5,-.3) {\ttfamily \scriptsize variant\textunderscore contig};
  % bounds
  \draw[densely dashed] (-1.4,0,-.5) -- (-1.4,4.9,-.5);
  \draw[densely dashed] (-1.2,0,-.5) -- (-1.2,4.9,-.5);
 \tikzcuboidset{front face/.style={fill=green!10},right face/.style={fill=green!10},top face/.style={fill=yellow!20}}
  \pic at (-1.4,0,-.5) {cuboid=.2--.9--0};
  \node at (-1.3,1.5,-.5) {\ttfamily \vdots};
  \pic at (-1.4,2,-.5) {cuboid=.2--.9--0};
  \pic at (-1.4,3,-.5) {cuboid=.2--.9--0};
  \pic at (-1.4,4,-.5) {cuboid=.2--.9--0};

 %% variant_position
  \node[rotate=90] at (-.8,2.5,-.3) {\ttfamily \scriptsize variant\textunderscore position};
  % bounds
  \draw[densely dashed] (-.7,0,-.5) -- (-.7,4.9,-.5);
  \draw[densely dashed] (-.5,0,-.5) -- (-.5,4.9,-.5);
 \tikzcuboidset{front face/.style={fill=green!10},right face/.style={fill=green!10},top face/.style={fill=yellow!20}}
  \pic at (-.7,0,-.5) {cuboid=.2--.9--0};
  \node at (-.6,1.5,-.5) {\ttfamily \vdots};
  \pic at (-.7,2,-.5) {cuboid=.2--.9--0};
  \pic at (-.7,3,-.5) {cuboid=.2--.9--0};
  \pic at (-.7,4,-.5) {cuboid=.2--.9--0};

 %% call_genotype
  \node at (2.0,5.3) {\ttfamily \scriptsize call\textunderscore genotype};
  % back box
  \draw[densely dashed] (0,0,-0.5) -- (3.9,0,-0.5);
  \draw[densely dashed] (0,0,-0.5) -- (0,4.9,-0.5);
  \draw[densely dashed] (0,4.9,-0.5) -- (3.9,4.9,-0.5);
  \draw[densely dashed] (3.9,0,-0.5) -- (3.9,4.9,-0.5);
 \tikzcuboidset{front face/.style={fill=blue!10},right face/.style={fill=green!10},top face/.style={fill=yellow!20}}
  \pic at (0,0) {cuboid=.9--.9--.5};
  \node at (0.45,0.5) {\ttfamily \tiny 100.0.0};
  \node at (0.5,1.6) {\ttfamily \vdots};
  \pic at (0,2) {cuboid=.9--.9--.5};
  \node at (0.45,2.5) {\ttfamily \tiny 2.0.0};
  \pic at (0,3) {cuboid=.9--.9--.5};
  \node at (0.45,3.5) {\ttfamily \tiny 1.0.0};
  \pic at (0,4) {cuboid=.9--.9--.5};
  \node at (0.45,4.5) {\ttfamily \tiny 0.0.0};
  \pic at (1,0) {cuboid=.9--.9--.5};
  \node at (1.45,0.5) {\ttfamily \tiny 100.1.0};
  \node at (1.5,1.6) {\ttfamily \vdots};
  \pic at (1,2) {cuboid=.9--.9--.5};
  \node at (1.45,2.5) {\ttfamily \tiny 2.1.0};
  \pic at (1,3) {cuboid=.9--.9--.5};
  \node at (1.45,3.5) {\ttfamily \tiny 1.1.0};
  \pic at (1,4) {cuboid=.9--.9--.5};
  \node at (1.45,4.5) {\ttfamily \tiny 0.1.0};
  \node at (2.5,0.5) {\ttfamily \dots};
  \node at (2.5,1.55) {\ttfamily $\ddots$};
  \node at (2.5,2.5) {\ttfamily \dots};
  \node at (2.5,3.5) {\ttfamily \dots};
  \node at (2.5,4.5) {\ttfamily \dots};
  \pic at (3,0) {cuboid=.9--.9--.5};
  \node at (3.45,0.5) {\ttfamily \tiny 100.10.0};
  \node at (3.5,1.6) {\ttfamily \vdots};
  \pic at (3,2) {cuboid=.9--.9--.5};
  \node at (3.45,2.5) {\ttfamily \tiny 2.10.0};
  \pic[ultra thick, red] at (3,3) {cuboid=.9--.9--.5};
  \node at (3.45,3.5) {\ttfamily \tiny 1.10.0};
  \pic at (3,4) {cuboid=.9--.9--.5};
  \node at (3.45,4.5) {\ttfamily \tiny 0.10.0};
  % front box
  \draw[densely dashed] (0,0) -- (3.9,0);
  \draw[densely dashed] (0,0) -- (0,4.9);
  \draw[densely dashed] (0,4.9) -- (3.9,4.9);
  \draw[densely dashed] (3.9,0) -- (3.9,4.9);
  
 %% dimensions
  \draw[stealth-stealth] (0.1,-0.2) -- (3.8,-0.2) node[midway,below] {\scriptsize samples};
  \draw[stealth-stealth] (4,-0.2, 0) -- (4,-0.2,-.5) node[midway,below right] {\scriptsize ploidy};
  \draw[stealth-stealth] (4.1,.1,-.5) -- (4.1,4.8,-.5) node[midway,below,rotate=90] {\scriptsize variants};

%% compresion
 \node (numcodecs) [rectangle, draw, densely dotted, thick, rounded corners, minimum width=2.4cm, minimum height=2.6cm, anchor= south west]
    at (4.8,2.2) {};
 \node[anchor=north,below] at (numcodecs.north) {\scriptsize Filter \& compress};
 \node[anchor=south,below] at (numcodecs.south) {numcodecs};
 \node (blosk) [rectangle, ultra thick, red, draw, rounded corners, minimum width=1.8cm, minimum height=1.6cm, anchor=center,align=center,text=black]
    at (numcodecs) {\scriptsize Blosc\\\scriptsize ZSTD\\\scriptsize Autoshuffle};
 \draw[ultra thick, red,-stealth] (3.9,3.5,-.25) -- (5,3.5,-.25);

%% storage
 \node (location) [rectangle, draw, densely dotted, thick, rounded corners, minimum width=2.4cm, minimum height=5cm, anchor= south west]
    at (7.4,1.1) {};
 \node[anchor=south,below] at (location.south) {Storage};
 \node[anchor=center] at (location) {
        \begin{forest}
          for tree={
            font=\tiny ,
            grow'=0,
            child anchor=west,
            parent anchor=south,
            anchor=west,
            calign=first,
            edge path={
              \noexpand\path [draw, \forestoption{edge}]
              (!u.south west) +(7.5pt,0) |- node[fill,inner sep=1.25pt] {} (.child anchor)\forestoption{edge label};
            },
            before typesetting nodes={
              if n=1
                {insert before={[,phantom]}}
                {}
            },
            fit=band,
            before computing xy={l=15pt},
          }
        [{\scriptsize Cloud, file or blob}
          [\ttfamily call\textunderscore genotype
            [\ttfamily 0.0.0]
            [\ttfamily ...]
            [\ttfamily 1.10.0, draw={red,ultra thick, rounded corners}]
            [\ttfamily ...]
            [\ttfamily 100.10.0]
          ]
          [\ttfamily sample\textunderscore id]
          [\ttfamily ...]
        ]
        \end{forest}
 };
 \draw[ultra thick, red, -stealth,rounded corners=5pt] (6.8,3.5,-.25) -- (8,3.5,-.25);
 
\end{tikzpicture} 



\end{document}