Graphviz

Draft

Definition

• Graphviz is an open source graph visualization software. It has several main graph layout programs, called layout engines.

dot

hierarchical drawings of directed graphs. The layout algorithm aims edges in the same direction (top to bottom, or left to right) and then attempts to avoid edge crossings and reduce edge length.

neato

spring model - attempts to minimize a global energy function, which is equivalent to statistical multi-dimensional scaling. See also fdp.

fdp

spring model layouts similar to those of neato, but does this by reducing forces rather than working with energy.

sfdp

multiscale version of fdp for the layout of large graphs.

twopi

radial layouts, The nodes are placed on concentric circles depending their distance from a given root node.

circo

circular layout - suitable for certain diagrams of multiple cyclic structures such as certain telecommunications networks

The GraphViz language and command line syntax

Command line syntax

See Command-line Invocation (at graphviz.org).

GraphViz includes several command line commands. The most imporant one is dot

The syntax pattern is:

cmd [ flags ] [ input files ]

Example:

dot -Tsvg GCF2.dot > GCF2.svg

Important flags:

-Tformat

-Tformat:renderer

-Tformat:renderer:formatter

Defines the output format. You also can choose from a renderer and change the default formatter for the renderer.

See the list of output formats.

Most important ones for web pages: png, svg, cmapx (client-side html map), imap (server-side html map) and vrml (partially supported)

Most important ones for printing: png, svg, ps, pdf

Most important ones for specialized clients: dot (reproduces the input, along with layout information for the graph), xdot (same with lots of additional information)

-Klayout_engine

Examples:

dot -Kneato is equivalent to running neato

dot -Ktwopi runs the radial twopi engine

-Gname[=value]

Defines attributes of the graph like overlaps, fonts, etc.

-ooutputfile

specify the output file. Otherwise it's written to default output.

Format, rendering engines, formatters and layout engines

Here are some examples

Client-side HTML maps

creates client-side image maps (of course you'll have to attache URLS to either nodes or edges or both)

Example:

dot -Tcmapx -oyour_graph.map -Tpng -oyour_graph.png your_graph.dot

Then use something like:

<IMG SRC="your_graph.png" USEMAP="#mainmap" /> 
... [content of your_graph.map] ... 

SVG output using the default dot layout engine

Default use:

dot -Tsvg file.dot

Create SVG output using the cairo renderer and formatter

dot -Tsvg:cairo:cairo file.dot

SVG output with the twopi engine

dot -Ktwopi -Tsvg GCF2.dot > GCF2.svg

PDF output with the twopi or fdp layout engines

dot -Ktwopi -Tpdf GCF2.dot > GCF2.pdf
dot -Kfdp -Tpdf GCF2.dot > GCF2.pdf

PNG output

Default use:

dot -Tpng 

specifies PNG output produced by Cairo formatted using the GD library:

dot  -Tpng:cairo:gd

xdot output

Pratical to see where nodes are being positioned so that you can manually change things

Also useful with graphviz clients

Example:

dot -Ksfdp -Txdot conole-fill-taxonomy-edutechwiki-sfdp.dot > temp.xdot

Some Neato command line examples

Lists configuration

neato -v

List all formats your installation can produce

neato -Tformat:

PNG output without overlap

neato -Tpng -Goverlap=false GCF.dot > GCF.png

SVG output

neato -Tsvg GCF.dot > GCF.svg
neato -Tsvg -Goverlap=scale -Gfontsize=8.0 GCF.dot > GCF.sv

Graph files

Graph file syntax

Below is a semi-formal grammar (i.e. the real grammar simplified):

Parentheses ( and ) indicate grouping when needed. Italic square brackets [ and ] enclose optional items. Vertical bars | separate alternatives. Stuff in bold must be typed "as is", e.g. bold [ ... ] square brackets or graph

graph	replace by	graph) id {statement-list}
statement-list	replace by	statement; statement; ...
statement	replace by	node-statement | edge-statement
id	replace by	id = id
attr-statement	replace by	node | edge) [attr-list ]
attr-list	replace by	id=id, id=id, ....
node-statement	replace by	id [ attr-list ]
id	replace by	quoted string
edge-statement	replace by	->) id [attr-list]

Comments

Are C++ style, i.e. either /* ....*/, // or #

Identifiers

• Must start with a letter
• Unquoted strings only can contain [A-Z][a-z][0-9] and "_"
• Otherwise strings must be quoted

Graphviz attributes

See either (or both):

• Graphviz attributes
• Node, Edge and Graph Attributes

We we understood right (this is a disclaimer!)

• You may these (most?) as global settings in the command line
• As global settings in a file
• As "parameter" for each node

size

defines the size of the output in inches

Consult Wikipedia's papersize or ISO 216 articles for pratical tables that translate ISO (European) A,B,C formats to inches.

Example of a portrait A2 page:

size="34.4,16.5";

ratio

Is a crucial attribute for larger graphs that should fit on a given canevas size

Example:

will try to fill a "page" defined by its size.

ratio="fill";

page

Defines multiple page outputs (only works with PS)

Example of A3 output (biggest page a typical laser printer can handle)

page="16.5,11.7" 

shape

Defines the shape of a none

Example of a node redition:

Remove shape (keep the text only), make it smaller:

node [fontsize=8,shape=none];

overlap

determines if and how node overlaps should be remove. There exist several alorithms

Examples:

overlap="false"
overlap="prism"

Some dot command line examples

Renders a (default) digraph in SVG with the default formatter

dot -Tsvg GCF2.dot > GCF2.svg

Simple graphviz for mediawiki examples

In this wiki, a directed graph that is represented like this (if you use the graphviz software, you should remove the XML tags).

<graphviz>
digraph G4 {
            "Learning theories" [URL="Learning theory"];
            "Pedagogic strategy" [URL="Pedagogic strategy"];
	    "Instructional design model" [URL="Instructional design model"];
            "Learning theories" -> "Pedagogic strategy";
            "Instructional design model" -> "Pedagogic strategy"
}
</graphviz>

could render like that (yes this wiki has a graphviz extension, but we may not keep it for sure since it is somewhat CPU intensive)

A simple non-directed graph (rendered with neato):

<graphviz renderer='neato' caption='Hello Neato'>
 graph G1 {
    aaa -- bbb;
    bbb -- c;
    aaa -- c;
}
</graphviz>

gives:

Or a more complex non-directed graph (rendered with neato):

<graphviz renderer='neato' caption='Hello Neato'>
graph G {
   run -- intr;
   intr -- runbl;
   runbl -- run;
   run -- kernel;
   kernel -- zombie;
   kernel -- sleep;
   kernel -- runmem;
   sleep -- swap;
   swap -- runswap;
   runswap -- new;
   runswap -- runmem;
   new -- runmem;
   sleep -- runmem;
}
</graphviz>

like this

Tools

See Graphviz - Graph Visualization Software (a longer list of interfaces, bindings, generators, scripts, etc.). Usually also needs graphviz software and the other way round. I.e. after installing Graphviz, you likely want to install a viewer or generator.

Mediawiki extensions

• GraphViz Widget for Mediawikis (alpha status in Feb 2008).
• Extension:Graphical Category Browser for MediaWiki (>1.7x). This may be outdated.
• http://www.mediawiki.org/wiki/Extension:GraphViz Extension:GraphViz] MediaWiki extension (Tested in this wiki. Worked with Mediawiki version 1.11, Graphviz 2.16.1 on Solaris 10 - DKS/2008)

GraphiViz Viewers

• ZGRViewer. GraphViz/DOT Viewer
• iDot - Incremental Dot Viewer
• "canviz" - HTML5 and Javascript

Installation

• Download of GraphViz software (source and Win/Linux binaries).

• Under Ubuntu I could install it through the package manager (there are quite a lot of dependencies).

sudo apt-get install graphviz

• For solaris, you can download a binary from sunfreeware.com plus these: cairo-1.4.10, freetype-2.3.1, glib-2.14.1, graphviz-2.16.1, pango-1.18.2, xrender-0.8.3,expat-2.0.1.

Tutorials and introductions

Manual

• Graphviz - Graph Visualization Software Includes both introductions and manuals (the HTML versions on top are better currently - Daniel K. Schneider 14:40, 20 July 2009 (UTC)).
• dot guide

Introductions

• Graphviz (Wikipedia)
• WikiSchool:Graphviz (Tutorial in German)
• An Introduction to GraphWiz, September 10th, 2004 by Mihalis Tsoukalos, Linux Journal

Graphviz for UML

• UML Diagrams Using Graphviz Dot. Explains how to create UML class diagrams.