FsnViz 0.3.0

Tool for plotting gene fusion events detected by various tools using Circos.

FsnViz

FsnViz is a Python tool for plotting RNA-seq fusion events using Circos plots. It parses outputs of gene fusion finding tools and creates Circos plots out of it.

Currently it accepts outputs of the following gene fusion finding tool:

• STAR-Fusion hits table (star-fusion)

• FusionCatcher final table (fusioncatcher)

Requirements

FsnViz is tested on the following Python versions:

• 3.5

• 3.6

and the following Circos versions:

• 0.69-2

Other Circos versions may be used but they are not guaranteed to work.

Installation

You can download the latest version via pip:

$ pip install fsnviz

Circos needs to be installed separately.

Usage

FsnViz needs only a result file of the gene fusion finding tool:

$ fsnviz star-fusion /path/to/result/file

With the invocation above, it will create the Circos plot as an SVG image called fsnviz.svg in the current directory. You can adjust the output behavior using some flags such as:

• The --output-dir flag to set the output directory. If it does not exist, it will be created for you.

• The --base-name flag to set the base name of the Circos plot (the default is fsnviz). Filename extensions are added accordingly.

• The --karyotype flag to set the Circos reference karyotype. Currently only human.hg19 and human.hg38 are available.

For a complete list, check out the help via fsnviz --help.

Credits

• Initial circos templates were based on the Circos templates of viewFusion, written by Jiang Li.

License

FsnViz is BSD-licensed. Refer to the LICENSE file for the full license.

Changelog

Versions 0.3

Release 0.3.0

release date: 14 August 2017

• Adds a new –circos-conf CLI flag which allows for custom circos config file.

• Updates the default template with bigger fonts

Versions 0.2

Release 0.2.0

release date: 30 January 2016

• Adds support for plotting FusionCatcher output.

Versions 0.1

Release 0.1.0

release date: 20 April 2016

• First release.

• Support for plotting STAR-fusion output on human.hg19 and human.hg38.