Dot Source Code Blocks in Org Mode

Introduction
Requirements and Setup
Org Mode Features for Dot Source Code Blocks
Examples of Use

Org Mode support for Dot

Introduction

Dot is one of six layout programs in the Graphviz open source graph visualization software, created at AT&T. The Graphviz layout programs take simple text graph descriptions and make useful diagrams in a variety of formats. Dot source code blocks call the dot layout program by default, but can be configured to call any of the other five Graphviz layout programs.

Graph visualization has applications in many technical domains, where it is often used to explore large data sets. A typical use in Org mode chains the dot source code block to a source code block in another language that is responsible for converting a data table into source code for one of the Graphviz layout languages.

Requirements and Setup

Graphviz is distributed on an open source basis under The Eclipse Public License. Executable packages from AT&T are available for Linux, Solaris, Windows, and Mac.

You can configure Org mode to execute dot source code blocks by adding a line to org-babel-load-languages:

(org-babel-do-load-languages
 'org-babel-load-languages
 '((dot . t))) ; this line activates dot

Optionally, graphviz-dot-mode offers font locking, indentation, and preview of graphs. The variable org-src-lang-modes can be customized to contain an entry that associates dot files with graphviz-dot-mode.

Org Mode Features for `Dot` Source Code Blocks

Header Arguments

Dot source code blocks produce graphics files. The default value for the :results header argument is "file" and for the :exports header argument it is "results".

There are two dot specific header arguments that can be used to tailor the command line. They are:

:cmd: this header argument can be used to change the layout program from the default "dot". Sensible values are "neato", "fdp", "sfdp", "twopi", and "circo".
:cmdline: the default sets the dot flag -T to the extension of the output file in order to indicate the output format. Graphviz recognizes three dozen output formats. Other flags that can be set with :cmdline control default graph, node, and edge attributes, among other functionality.

The :file header argument is required for dot source code blocks.

Sessions

Dot does not support sessions.

Result Types

Dot source code blocks produce graphic files, so the default value "file" is the only sensible type of result.

Other

Dot source code blocks currently do not evaluate variables.

Examples of Use

A typical use of a dot source code block is to produce a graph visualization of a data set. In this example, the following input table

a	Hello
b	World!

is passed to a source code block that is responsible for producing valid dot code

(mapcar #'(lambda (x)
            (princ (format "%s [label =\"%s\", shape = \"box\"];\n"
                           (first x) (second x)))) table)
            (princ (format "%s -- %s;\n" (first (first table)) (first (second table))))

#+name: make-dot
#+BEGIN_SRC emacs-lisp :var table=dot-eg-table :results output :exports none
  (mapcar #'(lambda (x)
              (princ (format "%s [label =\"%s\", shape = \"box\"];\n"
                             (first x) (second x)))) table)
              (princ (format "%s -- %s;\n" (first (first table)) (first (second table))))
#+END_SRC

and this is chained to a dot source code block

#+BEGIN_SRC dot :file images/test-dot.png :var input=make-dot :exports results
graph {
 $input
}
#+END_SRC

that wraps the input in a graph{} command to produce the following graphic output

graph {
 $input
}

An example of chaining source code blocks to produce a dot graph is provided by Schulte et al. in A Multi-Language Computing Environment for Literate Programming and Reproducible Research.