The graph below describes the Yeast Glycolytic pathway. The rendering information was generated by the JDesigner modeling environment and comes as an example SBML file with SBW.
Modifying the graph with PGF/TikZ
PGF/TikZ provides a wide array of methods to modify vector graphics. We can take advantage of this flexibility when we wish to draw attention to parts of certain reactions in our model diagrams in a few simple ways.
Say for instance that we wanted to draw the reader's attention to the ATP species in the model diagram of Yeast Glycolysis. One way to do this would be to change the gradient color of the species' node so that it stands out from all the other nodes. In addition, we can change the color of the arrows leading to ATP so that reactions generating ATP stand out.
PGF/TikZ Output
\documentclass{article}
\usepackage{tikz}
\usepackage{pgf}
\usepackage[total={1144pt,949pt}, centering, a2paper, landscape]{geometry}
\pagestyle{empty}
\begin{document}
\begin{center}
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% List of colors used:
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% List of gradients used:
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% Group for J8
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\draw[line width = 2pt, color = Color_2!100, ] (770.666666666667pt, 478pt) .. controls (768pt, 495pt) and (767pt, 486pt) .. (768pt, 523pt);
\draw[line width = 2pt, color = Color_2!100, ] (526.6pt, 562pt) .. controls (559pt, 520pt) and (767pt, 486pt) .. (768pt, 523pt);
}
{
% Group for J16
\draw[line width = 2pt, color = Color_2!100, ] (313pt, 179pt) .. controls (268pt, 177pt) and (268pt, 243pt) .. (485pt, 367.885654885655pt);
{
\pgftransformshift{\pgfpoint{ 485pt }{ 367.8857pt } }
\pgftransformcm { 0.8667153 }{ 0.4988032 }{ -0.4988032 }{ 0.8667153 }{\pgfpoint{ 0pt }{ 0pt } }
{
% LineEnding for ADP
{
% Polygon for ADP
\pgftransformshift{\pgfpoint{ -10pt }{ -5pt } }
\draw [line width = 2pt, color = Color_2!100, fill = Color_2!100 ]
(0pt,0pt)--(10pt,5pt)--(0pt,10pt)--(3.3pt,5pt)--(0pt, 0pt) -- cycle;
}
}
}
\draw[line width = 2pt, color = Color_2!100, ] (313pt, 179pt) .. controls (268pt, 177pt) and (259pt, 125pt) .. (236.142857142857pt, 100pt);
{
\pgftransformshift{\pgfpoint{ 236.1429pt }{ 100pt } }
\pgftransformcm { -0.6747693 }{ -0.7380288 }{ -0.7380288 }{ 0.6747692 }{\pgfpoint{ 0pt }{ 0pt } }
{
% LineEnding for Glycogen
{
% Polygon for Glycogen
\pgftransformshift{\pgfpoint{ -10pt }{ -5pt } }
\draw [line width = 2pt, color = Color_2!100, fill = Color_2!100 ]
(0pt,0pt)--(10pt,5pt)--(0pt,10pt)--(3.3pt,5pt)--(0pt, 0pt) -- cycle;
}
}
}
\draw[line width = 2pt, color = Color_2!100, ] (488.757575757576pt, 254pt) .. controls (405pt, 172pt) and (358pt, 181pt) .. (313pt, 179pt);
\draw[line width = 2pt, color = Color_2!100, ] (651pt, 185.643356643357pt) .. controls (532pt, 183pt) and (358pt, 181pt) .. (313pt, 179pt);
}
{
% Group for J17
\draw[line width = 2pt, color = Color_2!100, ] (859pt, 266pt) .. controls (862pt, 345pt) and (889pt, 395pt) .. (533pt, 382.597897503285pt);
{
\pgftransformshift{\pgfpoint{ 533pt }{ 382.5979pt } }
\pgftransformcm { -0.9993937 }{ -0.03481624 }{ -0.03481624 }{ 0.9993938 }{\pgfpoint{ 0pt }{ 0pt } }
{
% LineEnding for ADP
{
% Polygon for ADP
\pgftransformshift{\pgfpoint{ -10pt }{ -5pt } }
\draw [line width = 2pt, color = Color_2!100, fill = Color_2!100 ]
(0pt,0pt)--(10pt,5pt)--(0pt,10pt)--(3.3pt,5pt)--(0pt, 0pt) -- cycle;
}
}
}
\draw[line width = 2pt, color = Color_2!100, ] (859pt, 266pt) .. controls (862pt, 345pt) and (866pt, 350pt) .. (884.945945945946pt, 405pt);
{
\pgftransformshift{\pgfpoint{ 884.9459pt }{ 405pt } }
\pgftransformcm { 0.3256896 }{ 0.9454768 }{ -0.9454768 }{ 0.3256895 }{\pgfpoint{ 0pt }{ 0pt } }
{
% LineEnding for Trehalose
{
% Polygon for Trehalose
\pgftransformshift{\pgfpoint{ -10pt }{ -5pt } }
\draw [line width = 2pt, color = Color_2!100, fill = Color_2!100 ]
(0pt,0pt)--(10pt,5pt)--(0pt,10pt)--(3.3pt,5pt)--(0pt, 0pt) -- cycle;
}
}
}
\draw[line width = 2pt, color = Color_2!100, ] (529pt, 258.593333333333pt) .. controls (656pt, 188pt) and (856pt, 187pt) .. (859pt, 266pt);
\draw[line width = 2pt, color = Color_2!100, ] (699pt, 179.303867403315pt) .. controls (856pt, 136pt) and (856pt, 187pt) .. (859pt, 266pt);
}
{
% Group for J18
\draw[line width = 2pt, color = Color_2!100, ] (174pt, 527pt) .. controls (173pt, 455pt) and (225pt, 529pt) .. (485pt, 575.199306759099pt);
{
\pgftransformshift{\pgfpoint{ 485pt }{ 575.1993pt } }
\pgftransformcm { 0.9845775 }{ 0.1749491 }{ -0.1749491 }{ 0.9845774 }{\pgfpoint{ 0pt }{ 0pt } }
{
% LineEnding for NADH
{
% Polygon for NADH
\pgftransformshift{\pgfpoint{ -10pt }{ -5pt } }
\draw [line width = 2pt, color = Color_2!100, fill = Color_2!100 ]
(0pt,0pt)--(10pt,5pt)--(0pt,10pt)--(3.3pt,5pt)--(0pt, 0pt) -- cycle;
}
}
}
\draw[line width = 2pt, color = Color_2!100, ] (174pt, 527pt) .. controls (173pt, 455pt) and (171pt, 456pt) .. (176.08pt, 425pt);
{
\pgftransformshift{\pgfpoint{ 176.08pt }{ 425pt } }
\pgftransformcm { 0.1617141 }{ -0.9868376 }{ 0.9868376 }{ 0.1617144 }{\pgfpoint{ 0pt }{ 0pt } }
{
% LineEnding for Succinate
{
% Polygon for Succinate
\pgftransformshift{\pgfpoint{ -10pt }{ -5pt } }
\draw [line width = 2pt, color = Color_2!100, fill = Color_2!100 ]
(0pt,0pt)--(10pt,5pt)--(0pt,10pt)--(3.3pt,5pt)--(0pt, 0pt) -- cycle;
}
}
}
\draw[line width = 2pt, color = Color_2!100, ] (484pt, 489.734982332155pt) .. controls (226pt, 529pt) and (175pt, 599pt) .. (174pt, 527pt);
\draw[line width = 2pt, color = Color_2!100, ] (105.570247933884pt, 793pt) .. controls (136pt, 691pt) and (175pt, 599pt) .. (174pt, 527pt);
}
{
% Rectangle for GLCi
\pgftransformshift{\pgfpoint{ 656pt }{ 49pt } }
\def \wholeShape {(0pt,0pt) rectangle(37pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for ATP
\pgftransformshift{\pgfpoint{ 489pt }{ 259pt } }
\def \wholeShape {(0pt,0pt) rectangle(34pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for G6P
\pgftransformshift{\pgfpoint{ 658pt }{ 174pt } }
\def \wholeShape {(0pt,0pt) rectangle(34pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for ADP
\pgftransformshift{\pgfpoint{ 491pt }{ 370pt } }
\def \wholeShape {(0pt,0pt) rectangle(35pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for F6P
\pgftransformshift{\pgfpoint{ 655pt }{ 249pt } }
\def \wholeShape {(0pt,0pt) rectangle(32pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for F16bP
\pgftransformshift{\pgfpoint{ 651pt }{ 358pt } }
\def \wholeShape {(0pt,0pt) rectangle(44pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for AMP
\pgftransformshift{\pgfpoint{ 35pt }{ 238pt } }
\def \wholeShape {(0pt,0pt) rectangle(36pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for DHAP
\pgftransformshift{\pgfpoint{ 751pt }{ 447pt } }
\def \wholeShape {(0pt,0pt) rectangle(42pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for GAP
\pgftransformshift{\pgfpoint{ 604pt }{ 448pt } }
\def \wholeShape {(0pt,0pt) rectangle(36pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for NAD
\pgftransformshift{\pgfpoint{ 491pt }{ 474pt } }
\def \wholeShape {(0pt,0pt) rectangle(36pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for BPG
\pgftransformshift{\pgfpoint{ 604pt }{ 571pt } }
\def \wholeShape {(0pt,0pt) rectangle(35pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for NADH
\pgftransformshift{\pgfpoint{ 492pt }{ 568pt } }
\def \wholeShape {(0pt,0pt) rectangle(43pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for P3G
\pgftransformshift{\pgfpoint{ 604pt }{ 667pt } }
\def \wholeShape {(0pt,0pt) rectangle(34pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for P2G
\pgftransformshift{\pgfpoint{ 604pt }{ 729pt } }
\def \wholeShape {(0pt,0pt) rectangle(34pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for PEP
\pgftransformshift{\pgfpoint{ 604pt }{ 802pt } }
\def \wholeShape {(0pt,0pt) rectangle(32pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for PYR
\pgftransformshift{\pgfpoint{ 283pt }{ 799pt } }
\def \wholeShape {(0pt,0pt) rectangle(35pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for AcAld
\pgftransformshift{\pgfpoint{ 78pt }{ 800pt } }
\def \wholeShape {(0pt,0pt) rectangle(44pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 1pt, color = Color_0!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for GLCo
\pgftransformshift{\pgfpoint{ 819pt }{ 49pt } }
\def \wholeShape {(0pt,0pt) rectangle(41pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for CO2
\pgftransformshift{\pgfpoint{ 103pt }{ 856pt } }
\def \wholeShape {(0pt,0pt) rectangle(35pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for EtOH
\pgftransformshift{\pgfpoint{ 59pt }{ 391pt } }
\def \wholeShape {(0pt,0pt) rectangle(38pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for Glycerol
\pgftransformshift{\pgfpoint{ 864pt }{ 590pt } }
\def \wholeShape {(0pt,0pt) rectangle(54pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for Glycogen
\pgftransformshift{\pgfpoint{ 190pt }{ 71pt } }
\def \wholeShape {(0pt,0pt) rectangle(60pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for Trehalose
\pgftransformshift{\pgfpoint{ 860pt }{ 412pt } }
\def \wholeShape {(0pt,0pt) rectangle(62pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Rectangle for Succinate
\pgftransformshift{\pgfpoint{ 148pt }{ 394pt } }
\def \wholeShape {(0pt,0pt) rectangle(62pt,24pt)}
\fill[rounded corners = 5pt, shading = LinearGradient_0, shading angle = -90 ] \wholeShape;
\draw[line width = 3pt, color = Color_1!100, rounded corners = 5pt ] \wholeShape;
}
{
% Group for sGlyph_0
\draw (674.5pt, 61pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { GLCi };
}
{
% Group for sGlyph_1
\draw (506pt, 271pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { ATP };
}
{
% Group for sGlyph_2
\draw (675pt, 186pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { G6P };
}
{
% Group for sGlyph_3
\draw (508.5pt, 382pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { ADP };
}
{
% Group for sGlyph_4
\draw (671pt, 261pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { F6P };
}
{
% Group for sGlyph_5
\draw (673pt, 370pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { F16bP };
}
{
% Group for sGlyph_6
\draw (53pt, 250pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { AMP };
}
{
% Group for sGlyph_7
\draw (772pt, 459pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { DHAP };
}
{
% Group for sGlyph_8
\draw (622pt, 460pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { GAP };
}
{
% Group for sGlyph_9
\draw (509pt, 486pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { NAD };
}
{
% Group for sGlyph_10
\draw (621.5pt, 583pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { BPG };
}
{
% Group for sGlyph_11
\draw (513.5pt, 580pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { NADH };
}
{
% Group for sGlyph_12
\draw (621pt, 679pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { P3G };
}
{
% Group for sGlyph_13
\draw (621pt, 741pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { P2G };
}
{
% Group for sGlyph_14
\draw (620pt, 814pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { PEP };
}
{
% Group for sGlyph_15
\draw (300.5pt, 811pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { PYR };
}
{
% Group for sGlyph_16
\draw (100pt, 812pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { AcAld };
}
{
% Group for sGlyph_17
\draw (839.5pt, 61pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { GLCo };
}
{
% Group for sGlyph_18
\draw (120.5pt, 868pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { CO2 };
}
{
% Group for sGlyph_19
\draw (78pt, 403pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { EtOH };
}
{
% Group for sGlyph_20
\draw (891pt, 602pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { Glycerol };
}
{
% Group for sGlyph_21
\draw (220pt, 83pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { Glycogen };
}
{
% Group for sGlyph_22
\draw (891pt, 424pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { Trehalose };
}
{
% Group for sGlyph_23
\draw (179pt, 406pt) node[text = Color_1!100, font = \fontsize{ 11 } { 11 }\fontfamily\sfdefault\selectfont] { Succinate };
}
}
\end{tikzpicture}
\end{center}
\end{document}