The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:
Common uses of the tool include:
Circleator...
First, install Circleator. After installing Circleator and its prerequisites, running the program requires as little as:
Examples of both of these types of files can be found in the Circleator source distribution. For example, from the top level of the unpacked Circleator zip or tar file the following command will create a Circleator figure for CM000961.gbk, which contains the genome of Corynebacterium genitalium ATCC 33030:
circleator --data=data/CM000961.gbk --config=conf/genes-percent-GCskew-1.cfg > fig1.svg
The resulting SVG file, fig1.svg
can be viewed directly in many
recent web browsers or image viewers. Or, if the Apache Batik
package has been installed, it can be used to convert the image to
PDF, PNG, or JPEG, using a wrapper script (rasterize-svg) from the
Circleator distribution:
rasterize-svg fig1.svg pdf
rasterize-svg fig1.svg png
rasterize-svg fig1.svg jpeg
The Circleator configuration file format aims to make the common case fast and the uncommon case possible. In other words, new users should be able to quickly produce a standard visualization of their data, provided it is in a commonly-used format. Conversely, experienced users should be able to create intricately-customized figures by using the same configuration file syntax.
genes
by itself on a line in the configuration file will display a circular track in which each gene is rendered as a curved black rectangle.genes color1=red
will behave the same as genes
, but using red instead of black.Circleator is Copyright (C) 2010-2017, Jonathan Crabtree \<jonathancrabtree@gmail.com>
Circleator is free software and is distributed under the terms of the Artistic License 2.0. For details, see the full text of the license in the file LICENSE in the top-level of this distribution.
Files with different licenses or copyright holders:
Copyright (c) 2002 Cynthia Brewer, Mark Harrower, and The Pennsylvania State University. The color specifications in this file are covered by an Apache-Style license. Please see the license statement in the file for details. The file itself was prepared by Martin Krzywinski and downloaded from http://mkweb.bcgsc.ca/brewer/swatches/brewer.txt
This product includes color specifications and designs developed by Cynthia Brewer (http://colorbrewer.org).
An Applications Note describing Circleator has been published in Bioinformatics:
Crabtree, J., Agrawal, S., Mahurkar, A., Myers, G.S., Rasko, D.A., White, O. (2014) Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG. Bioinformatics, 10.1093/bioinformatics/btu505.