Visualisations in Galaxy

Authors:

Helena Rasche

Saskia Hiltemann

Updated:

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Requirements

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Introduction to Galaxy Analyses

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What is Data Visualisation

Making graphics to clearly convey data
Many different options

Selection of numerous graph types include pie, dot, bar, line charts, map and guages.

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What is Data Visualisation

More than just scatter plots and bar charts
Many domain-specific
- Protein folding, network graphs, trees, genome browsers

Examples of 6 different visualisations in galaxy features an MSA, a couple graphs, RNA structure, and 3d visualisations of proteins

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Why visualizations?

"A picture is worth 1000 words"
Anscombe's Quartet

All these datasets share the same basic statistics:

X mean: 54.26, X SD: 16.76
Y mean: 47.83, Y SD: 26.93
Correlation: -0.06

But visualisation reveals vastly different underlying structures!

Animated gif cycling through Anscombe's quartet and various variations that all have the same mean, SD, and correlation but look vastly different to someone's eyes.

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Anscombes quartet, all these datasets have same mean, standard deviation and correlation, yet when visualizing them it is revealed they have vastly different structures.

Data Visualisation in Galaxy

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Genome Browsers

Visualize the genome
- mapped sequence reads, variants, genes, ..

JBrowse screenshot

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Genome Browsers in Galaxy

As display applications
- e.g. UCSC browser, IBV, IGB, ..
- accessed via links on dataset

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JBrowse

Genome browser as a regular tool
Configure your settings

Screenshot of Galaxy showing the configuration interface for JBrowse.

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JBrowse is not a display application like the previous examples
Regular Galaxy tool

JBrowse

Then interactively explore your genome

Screenshot of JBrowse showing sequence, some bar charts, a SNP map highlighting snps, and aligned reads.

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Galaxy Charts

Accessed through Charts icon galaxy-barchart on dataset
Different options depending on datatype

Example of list of Galaxy charts

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Galaxy Charts

After selecting chart type, can customize settings
Example: Protein Viewer

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Visualisation Tools

Many tools for visualisation
Example: Circos for circular data plots

Sample Circos images

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Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Authors:

Helena Rasche

Saskia Hiltemann

This material is licensed under the Creative Commons Attribution 4.0 International License.

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Visualisations in Galaxy

Requirements

What is Data Visualisation

What is Data Visualisation

Why visualizations?

Data Visualisation in Galaxy

Genome Browsers

Genome Browsers in Galaxy

JBrowse

JBrowse

Galaxy Charts

Galaxy Charts

Visualisation Tools

Related tutorials

Thank You!

Requirements

Help