GraphViz Example: b457.dot

graph G {

overlap=false; //scale; //false; //

directed=false;

pack=true; // put unconnected subgraphs as close as possible;

center=true; // center on page

//minsep=0.2;

size="7,10"; //"6,9";

ratio=0.6; // aspect ratio

fontsize=14;

// outputorder=edgesfirst; // make nodes come out on top;

// set up default shape for nodes;

node [ shape=rectangle, style=filled,

fillcolor=gray80, color=gray80,

fixedsize=true, height=0.25, width=1,

fontcolor=black, fontsize=14];

// Default edge characteristics

edge [color="blue", len=0.1, fontsize=16, arrowhead="dot", arrowtail="dot", arrowsize=0.4];

"S0001126" [URL="javascript:ShowNodeContents('\N')", tooltip="STE12/YHR084W/S0001126", fillcolor="red", color="red", label="STE12"];

label = "Query genes: STE12 (YHR084W/S0001126)\lThis graph produced by BioTrawler,\la BioMOBY (web-service)-based application for viewing distributed gene/protein interaction data,\lpart of the BioGraphNet initiative at the Roth Lab, Harvard Medical School.\l\l";

"Legend here" [fixedsize=false, fontsize=14, shape="rectangle", label=<InteractionColorCorrelatedCoexpression GavinSpoke getKnownRegulatorsAndTargets Homology SyntheticLethal >];

"S0001126" -- "S0003268" [color="green", style="setlinewidth(1)", len=1, URL="", label=""];

"S0001126" -- "S0003057" [color="blue", style="setlinewidth(1)", len=1, arrowsize="1", arrowhead="vee", arrowtail="none" , URL="", label=""];

"S0001126" -- "S0001868" [color="blue", style="setlinewidth(1)", len=1, arrowsize="1", arrowhead="vee", arrowtail="none" , URL="", label=""];

"S0001126" -- "S0000532" [color="blue", style="setlinewidth(1)", len=1, arrowsize="1", arrowhead="vee", arrowtail="none" , URL="", label=""];

"S0001868" [URL="javascript:ShowNodeContents('\N')", tooltip="STE2/YFL026W/S0001868", fillcolor="gray80", color="gray80", label="STE2"];

"S0003057" [URL="javascript:ShowNodeContents('\N')", tooltip="MF(ALPHA)2/YGL089C/S0003057", fillcolor="gray80", color="gray80", label="MF(ALPHA)2"];

"S0003268" [URL="javascript:ShowNodeContents('\N')", tooltip="CAX4/YGR036C/S0003268 (CWH8)", fillcolor="gray80", color="gray80", label="CAX4"];

"S0000532" [URL="javascript:ShowNodeContents('\N')", tooltip="FUS1/YCL027W/S0000532", fillcolor="gray80", color="gray80", label="FUS1"];

// Use epsilon, maxiter to make sure the graph renders quickly,

// no matter how many nodes are present.

// If there are few, the rendering will be good even with loose parameters

// If there are many, it won't matter too much how good the layout is,

// the user won't be able to read it anyway.

// The important thing is to give a quick response.

epsilon=0.0004;

maxiter=10000;

overlap=scale;

};

Done