Visualizations: JavaScript Plugins

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# Visualizations: JavaScript Plugins

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<ul class="text-list">
			
			<li>
				<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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				<a href="/training-material/hall-of-fame/yhoogstrate/" class="contributor-badge contributor-yhoogstrate"><img src="https://avatars.githubusercontent.com/yhoogstrate?s=36" alt="Youri Hoogstrate avatar" width="36" class="avatar" />
    Youri Hoogstrate</a>
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				<a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a>
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				<a href="/training-material/hall-of-fame/guerler/" class="contributor-badge contributor-guerler"><img src="https://avatars.githubusercontent.com/guerler?s=36" alt="Aysam Guerler avatar" width="36" class="avatar" />
    Aysam Guerler</a>
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				<a href="/training-material/hall-of-fame/dannon/" class="contributor-badge contributor-dannon"><img src="https://avatars.githubusercontent.com/dannon?s=36" alt="Dannon Baker avatar" width="36" class="avatar" />
    Dannon Baker</a></li>
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### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- How can I make a custom JavaScript plugin?

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn how to add custom JavaScript plugins using the Galaxy Charts framework

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# Javascript Plugin Development in Galaxy

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## Tutorial Overview

- Why visualization?

- What are the available visualization types and which one should I use?

- Introduction to Charts

- Step-by-step guide to adding new visualizations

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## Why visualizations?

![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.](../../images/anscombe-quartet-animated.gif)

```python
X mean: 54.26, X SD: 16.76
Y mean: 47.83, Y SD: 26.93
Corr: -0.06
```

???
Anscombe's 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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## Types of visualizations in Galaxy

- **Trackster** - built-in genome browser
- **Display applications**
  - UCSC Genome Browser
  - IGV
- **Galaxy tools**
  - JBrowse
  - Krona
- **Visualization plugins**
  - Charts
  - Generic
- **Interactive Environments**
  - Jupyter/Rstudio
  - IOBIO (bam/vcf visualizations)
  - Phinch (metagenomics visualizations)

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## Which should I use?

![Flowchart. Only available on an external website? If yes use a display application. Does it need to be served (e.g. python), if yes use an interactive tool. Is it computationally intensive, then it needs to be a regular tool. Is it written in javascript? Then it shold be a generic plugin. If it passes all these tests it can be a charts plugin.](../../images/which_viz_flowchart.png)

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## Charts Visualization Framework

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## Charts
A shared interface for a wide range of pure JavaScript visualization types i.e.
bar diagrams, pie charts, scatter plots, heat maps and others.

![Montage of several charts, bar, dot, stacked bar/line, box and whisker, and doughnut charts.](../../images/charts_examples.png)

Reference: [https://www.nvd3.org ](https://www.nvd3.org), [https://www.jqplot.com ](https://www.jqplot.com)

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## Chart Configuration - Bar chart example

![A tool form with bar chart options shown on left and right.](../../images/charts_bar_config.png)

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If a plugin is unavailable, custom visualization types like this heat map here can be added.

![A large zoomed out heatmap is shown with an inset highlighting a small portion.](../../images/charts_heatmap.png)

Charts is able to pre-process large-scale data behind the scenes.

Showing Protein-Protein Interaction data from [http://www.compsysbio.org/bacteriome/ ](http://www.compsysbio.org/bacteriome/).

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## Charts - PDB viewer example

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

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![Examples of 6 different visualisations in galaxy features an MSA, a couple graphs, RNA structure, and 3d visualisations of proteins](../../images/charts_examples2.png)

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## Community-driven plugins

![Montage of several logos include D3, jqPlot, BioJS, Cytoscape, and NVD3.](../../images/charts_community.png)

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## Video Example

[![Video demonstrating several viz plugins.](../../images/charts_video.png)](https://vimeo.com/222709200)

???
click the image to run the video

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

- Charts is a pluggable extension system for JS-only visualizations

- With three key files we can integrate any JS-only visualization into Galaxy

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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/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><a href="/training-material/hall-of-fame/yhoogstrate/" class="contributor-badge contributor-yhoogstrate"><img src="https://avatars.githubusercontent.com/yhoogstrate?s=36" alt="Youri Hoogstrate avatar" width="36" class="avatar" />
    Youri Hoogstrate</a><a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a><a href="/training-material/hall-of-fame/guerler/" class="contributor-badge contributor-guerler"><img src="https://avatars.githubusercontent.com/guerler?s=36" alt="Aysam Guerler avatar" width="36" class="avatar" />
    Aysam Guerler</a><a href="/training-material/hall-of-fame/dannon/" class="contributor-badge contributor-dannon"><img src="https://avatars.githubusercontent.com/dannon?s=36" alt="Dannon Baker avatar" width="36" class="avatar" />
    Dannon Baker</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/nsoranzo/" class="contributor-badge contributor-badge-small contributor-nsoranzo"><img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo 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/dannon/" class="contributor-badge contributor-badge-small contributor-dannon"><img src="https://avatars.githubusercontent.com/dannon?s=36" alt="Dannon Baker avatar" width="36" class="avatar" /></a><a href="/training-material/hall-of-fame/gallardoalba/" class="contributor-badge contributor-badge-small contributor-gallardoalba"><img src="https://avatars.githubusercontent.com/gallardoalba?s=36" alt="Cristóbal Gallardo 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><a href="/training-material/hall-of-fame/njall/" class="contributor-badge contributor-badge-small contributor-njall"><img src="https://avatars.githubusercontent.com/njall?s=36" alt="Niall Beard avatar" width="36" class="avatar" /></a><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/bebatut/" class="contributor-badge contributor-badge-small contributor-bebatut"><img src="https://avatars.githubusercontent.com/bebatut?s=36" alt="Bérénice Batut avatar" width="36" class="avatar" /></a></td>
	</tr>

</table>

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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/>