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 runs on Python 3.5 and was tested on Circos 0.69-2. Other Circos versions may or may not 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 isfsnviz
). Filename extensions are added accordingly.- The
--karyotype
flag to set the Circos reference karyotype. Currently onlyhuman.hg19
andhuman.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.