Circos

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# Circos

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			<li>
				<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a>
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				<a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" />
    Saskia Hiltemann</a></li>
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Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

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### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- What is Circos?

- How can I use Circos within Galaxy?

- What are some of the different track types I can plot?

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# Circos for Genomics Visualisation

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### What is Circos?

- Circular Graphics
- Highly flexible, but also very complex configuration
- ... but beautiful visualisations
- Can visualise a huge range of data types

![Panel of example Circos images](../../images/circos-sample-panel.png)

???
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.

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### Circos in Galaxy

- Tool that produces a Circos Plot (PNG / SVG)
- Circos is too complex to put all configuration options in Galaxy
    - Option to **download full configuration** directory
        - allows for further manual tweaking locally
        - 90% done inside Galaxy, last 10% finished locally

.image-50[![Screenshot of the Circos Galaxy tool](../../images/circos/circos_tool.png)]

???
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.)

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### Supported Features

- Covers *most* of the possibilities of Circos
- Can **auto convert** GFF3/BED/(big)Wig datasets into appropriate formats
- Supports common Circos features like:
	- histograms
	- heatmaps
	- "tile" (from gff3/bed)
	- line
	- scatter
	- ribbons
- Complex Circos visualisations made easy (Thanks Galaxy!)

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### Tracks: Histograms

- For data which associate a position with a value
- Can be good for
  - Gene density on large genomes
  - Variation density?
  - GC Skew

![Histogram Plot](../../images/circos-histogram.png)

???

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### Tracks: Heatmaps

- Similar use case to histograms
- Histograms may provide easier quantification for viewers

![Heatmap Plot](../../images/circos-heatmap.png)

???

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

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### Tracks: Tiles

- Show genomic regions
- Great for genes on small genomes

![Tile Plot](../../images/circos-tiles.png)

???
"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)

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### Tracks: Scatter

- Can be used similarly to heatmaps and histograms

![Scatter Plot](../../images/circos-scatter.png "The data are SNP density for windows of 100kb (number of SNPs from dbSNP per base).")

???

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

http://circos.ca/documentation/tutorials/2d_tracks/scatter_plots/lesson

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### Tracks: Lines

![Line Plot](../../images/circos-line.png)

???

Image is based off of the Circos Line lesson.

http://circos.ca/documentation/tutorials/2d_tracks/line_plots/images

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### Tracks: Ribbons

- Shows a relationship between two regions
- On the same chromosome or on different ones
- Great for synteny mapping or other regional interactions

![Ribbon Plot](../../images/circos-ribbons.png)

???

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.

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### Circos: An iterative process!

- Because of its complexity, creating a Circos plot is often an *iterative* process
- Build your plot one step at a time, check the output regularly!

.image-40[![Gif of a circos plots through the development process](../../images/circos2.gif)]

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### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- Circos is very powerful, but also very complex

- Creating plots is an iterative process

- The full configuration directory can be downloaded from Galaxy to be further tweaked locally

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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<table class="contributions">
	
	<tr>
		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a><a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" />
    Saskia Hiltemann</a>
		</td>
	</tr>

<tr class="reviewers">
		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
		<td>
			<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-badge-small contributor-hexylena"><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-badge-small contributor-abretaud"><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-badge-small contributor-shiltemann"><img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-badge-small contributor-bgruening"><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" /></a></td>
	</tr>

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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>