View markdown source on GitHub




last_modification Published: Jan 10, 2020
last_modification Last Updated: Oct 23, 2023

Circos for Genomics Visualisation

What is Circos?

Panel of example Circos images

Speaker Notes Many researchers find Circos overwhelming and complex. This tool can save them time and we will hopefully show them how to reproduce several plots from published papers.

Circos in Galaxy

.image-50[Screenshot of the Circos Galaxy tool]

Speaker Notes Emphasize that producing production quality plots is still a lot of work. Not all configuration options available in Circos can be set in the Galaxy tool. But all the config files can be downloaded so that you can tweak the plot manually if you have circos installed on your computer

We cannot support them uploading these edited config files into Galaxy because of potential security issues (circos can shell out.)

Supported Features

Tracks: Histograms

Histogram Plot

Speaker Notes

Tracks: Heatmaps

Heatmap Plot

Speaker Notes

It can be easier to quantify differences between two values next to each other with the histogram than relying on the viewer’s ability to distinguish + quantify how far apart two colours lie on a colour scale. These can be pretty but are harder to extract data from

Tracks: Tiles

Tile Plot

Speaker Notes “Tile tracks are used to show spans such as genomic regions (genes, exons, duplications) or coverage elements (clones, sequence reads). Tiles will stack within their track to avoid overlap.” (circos documentation)

Tracks: Scatter

Scatter Plot

Speaker Notes

Image is based off of the Circos Scatter plot lesson. All images in this tutorial should be reproducible with the Galaxy Circos tool

Tracks: Lines

Line Plot

Speaker Notes

Image is based off of the Circos Line lesson.

Tracks: Ribbons

Ribbon Plot

Speaker Notes

This plot highlights all interactions coming from, or going to chr1.

This plot was generated from a set of random links. The circos-tools package includes a randomlinks tool that will generate these files. There is no galaxy wrapper for this tool.

Circos: An iterative process!

.image-40[Gif of a circos plots through the development process]

Key Points

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.