Visualisations in Galaxy

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# Visualisations in Galaxy

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  <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>
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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.](../../images/chart_types.png)

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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](../../../dev/images/charts_examples2.png)

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## Why visualizations?

.pull-left[
- *"A picture is worth 1000 words"*

- Anscombe's Quartet

- All these datasets share the same basic statistics:

```python
  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!
]
.pull-right[
.image-90[![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.](../../../dev/images/anscombe-quartet-animated.gif)]
]

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

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## Data Visualisation in Galaxy

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## Genome Browsers

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

![JBrowse screenshot](../../images/jbrowse/sequencing.png)

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## Genome Browsers in Galaxy

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

![screenshot of display options](../../images/display_options_bam.png)

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## JBrowse

- Genome browser as a regular tool
- Configure your settings

.image-75[ ![Screenshot of Galaxy showing the configuration interface for JBrowse.](../../images/jbrowse_tool.png) ]

???

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

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## JBrowse

- Then interactively explore your genome

.image-75[![Screenshot of JBrowse showing sequence, some bar charts, a SNP map highlighting snps, and aligned reads.](../../images/jbrowse/sequencing.png)]

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## Galaxy Charts

- Accessed through Charts icon <i class="fas fa-chart-column" aria-hidden="true"></i><span class="visually-hidden">galaxy-barchart</span> on dataset
- Different options depending on datatype

![Example of list of Galaxy charts](../../images/charts_list.png)

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## Galaxy Charts

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

![Configuration for the protein viewer is shown on the left, a 3d structure of a protein shown on the right](../../../dev/images/charts_pdbviewer.png)

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## Visualisation Tools

- Many tools for visualisation
- Example: Circos for circular data plots

![Sample Circos images](../../images/circos-sample-panel.png)

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## Related tutorials

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