Graphviz: Difference between revisions

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[[Category: Visualization]]
[[Category: Visualization]]
[[Category:Mediawiki documentation]]
[[Category:Mediawiki documentation]]
==Related Links:==
[http://www.noxedge.com/'''nitric oxide''']

Revision as of 11:59, 30 May 2010

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). See the official doc for a complete one.

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 --> (digraph ¦ graph) id {statement-list}
statement-list --> statement; statement; ...
statement --> attr-statement ¦ node-statement ¦ edge-statement
node-statement --> id [ attr-list ]
attr-statement --> (graph ¦ node ¦ edge) [attr-list ]
id --> id = id
attr-list --> id=val_id, id=val_id, ....
id --> String ¦ quoted string
edge-statement --> id (-- ¦ ->) id [attr-list]
Comments

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

Identifiers (id and val_id)
  • 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):

In addition.

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 at the graph level or for all nodes or for all edges.
  • As "parameter" for node statements
  • As "parameter" for edge statements

Also, some will not work with certain layout programs and there is interaction. I.e. sometimes it's quite difficult to figure out what given attributes will do. I found that pinning down nodes in given locations won't work with sfdp (or maybe I didn't figure out how to do this ...) - Daniel K. Schneider 13:46, 24 May 2010 (UTC).

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 as standalone program, you should remove the XML tags with are specific to the Graphviz mediawiki extension we are using here). 

<graphviz>
digraph G4 {
            node [fontsize="10"];
            "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 (Notice: the XML attributes are ignored, worked once with an older version that is lost to humanity: 

<graphviz>
 graph G1 {
    aaa -- bbb;
    bbb -- c;
    aaa -- c;
}
</graphviz>

gives:

Or a more complex non-directed graph: 

<graphviz>
graph G7 {
   node [fontsize="8"];
   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

GraphiViz Viewers

Installation

Windows
  • Download of GraphViz software (source and Win/Linux binaries).
  • The windows version has a *.msi installer. For VISTA, a command-line install is recommended, but I had to run the "click-on-it" install in order to have the gui tools through the command menu. Anyhow, it works fine both under VISTA and Win7
Ubuntu 32-bit Desktop
  • Under Ubuntu I could install it through the package manager (there are quite a lot of dependencies). However you will get an old version that doesn't include the very useful sfdp layout engine.
sudo apt-get install graphviz
  • For my Ubuntu 10.04 LTS - the Lucid Lynx, I got both graphviz_2.26.3-1_i386.deb and libgraphviz4_2.26.3-1_i386.deb and installed it on top of it. Works. - Daniel K. Schneider 15:39, 25 May 2010 (UTC)
Ubunto 64-bit server

Download (as of May 2010): 

wget http://www.graphviz.org/pub/graphviz/stable/ubuntu/ub9.04/x86_64/graphviz_2.26.3-1_amd64.deb
wget http://www.graphviz.org/pub/graphviz/stable/ubuntu/ub9.04/x86_64/libgraphviz4_2.26.3-1_amd64.deb

Install: 

pkg -i libgraphviz4_2.26.3-1_amd64.deb 
dpkg -i graphviz_2.26.3-1_amd64.deb

Since it is is likely that libraries are missing, type the following that should fix everything, i.e. retrieve missing stuff and install everything :) 

apt-get -f install

Note: Again, you will have to do this manually since the graphviz in the official Ubuntu install is old (sfdp layout engine missing)

Solaris
  • For solaris, you can download a binary from sunfreeware.com plus these (check the version dependencies): cairo-xxx, freetype-xxx, glib-xxx, graphviz-xxx, pango-xxx, xrender-xxx, expat-xxx.

Tutorials and introductions

Manual
Introductions
Graphviz for UML
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