Generic plugins

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# Generic plugins

<div class="contributors-line">
		
	
<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>
			<li>
				<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></li>
</ul>

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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- Javascript knowledge

---

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

- How can visualization plugins benefit science?

---

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

- Implement a first Galaxy visualization

- Understand the client side vs. server side principle

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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
```

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

---

## Why visualizations?

Bam files - textual

![Screenshot of a terminal showing a wall of text with lines from a BAM file](../../images/vis_alignment_plaintext.png)

---

## Why visualizations?

Bam files - visualized

![Screenshot of IGV with presumably the same bam file from before showing a large gap in the alignment, now clear due to a visualisation.](../../images/vis_alignment.png)

---

## 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)

---

## 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)

---

## Plugins

- Visualizations button on history items
- Different options depending on file type

![Screenshot of the history in galaxy with viz dropdown clicked. On one dataset the options are charts and scatterplots for a tabular dataset. On the other is 'visualise in trackster' for a BAM dataset](../../images/vis_plugin_menu.png)

---

.enlarge120[
## Plugins: Charts
]
.pull-left[
![Charts selection interface showing a number of chart types that can be selected](../../images/vis_charts_02.png)
]

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

---

## Plugins: Charts

- Allows exporting screenshots

![A screenshot button is clicked providing optinos to save as PNG, SVG, or PDF](../../images/vis_charts_05.png)

- For more information, see the charts plugin development
[slides](/training-material/topics/dev/tutorials/visualization-charts/slides.html) and [tutorial](/training-material/topics/dev/tutorials/visualization-charts/tutorial.html)
---

## Plugins: Generic

- Elements of visualization plugin:
    * Configuration (name, description, datatype)
    * Template
    * Static resources (js, css, images)

- Project Structure
    * located in `$GALAXY_ROOT/config/plugins/$PLUGIN_NAME`

```
                myviz
                ├── config
                │   └── myviz.xml
                ├── static
                │   ├── css
                │   ├── img
                │   └── js
                └── templates
                    └── myviz.mako
```
---

## Plugins: XML file

```bash
$ touch $GALAXY_ROOT/config/plugins/$PLUGIN_NAME/config/$PLUGIN_NAME.xml
```

- Hooks visualizations into Galaxy

![Screenshot of code with boxes highlighting Draw RNA.js and the datatypes that it can accept. A template drawrnajs.mako is also highlighted](../../images/vis_plugin_conf_xml.png)

* Data types must match with class names in `$GALAXY_ROOT/lib/galaxy/datatypes/`

---

## Plugins: Mako file

- For templates of HTML files:
```bash
$ touch $GALAXY_ROOT/config/plugins/$PLUGIN_NAME/templates/$PLUGIN_NAME.mako
```
- Link to data types and HTML template file
    * Every invocation of visualization: template compiled

![Screenshot of more code showing a mako template being rendered](../../images/vis_mako_hello_world_dual.png)

---

## Plugins: Mako file

- Access to the history item (*hda*) **pre** template compilation:
    * `$hda.file_name`
    * `$hda.metadata.dbkey`
    * Avoid (unnecessary) copies of whole files
- Access to *hda* **post** template compilation -> via URLs
    * Download data file by browser (client side)
        - Inconvenient for large files:
            * Indices and query protocols (e.g. DAS protocol)
    * Resolving history uid to hash
    * Correction for extended root URLs:

![Screenshot of a URL bar reading https://bioinf-galaxian.erasmusmc.nl/galaxy/](../../images/vis_nested_url.png)

---

## Plugins: Mako syntax

- Access to *hda* **post** template compilation:
    - Obtain hash value used in urls *hdadict['id']*
    - Essential Python variables:

![A mako template with a python codeblock section highlighting hdadict, root, app_root, file_url](../../images/vis_important_variables.png)

---

## Plugins:  Javascript and jQuery

- HTML / JS implementation make often use of jQuery
    * Galaxy ships with jQuery

```html
<script type="text/javascript" src="${root}/static/scripts/libs/jquery/jquery.js" />
```

---

## Plugins: Generic template

![Another code screenshot showing a generic template that can be used for viz.](../../images/vis_generic_template.png)

---

### Plugins: Static files

- External libraries and static files go in `./static` dir:

![Code screenshot showing a cool_vis_plugin.js being loaded](../../images/vis_generic_template_static.png)
![Screenshot of its location in the static directory.](../../images/vis_static_dir.png)

---

## Plugins: Summary

- Galaxy visualization plugins:
    * Datatype-specific
    * Written in HTML5 / JS
    * Require minor python / Galaxy ecosystem knowledge
    * Have access to the whole Galaxy system
        - pre-compilation: python
        - post-compilation: JS / API
    * Can be installed without additional configuration
    * Can not be connected to workflows
    * Can not (out of the box) save and share

---

## Plugins: More tips and tricks

- Galaxy has UI guidelines with corresponding CSS (https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook)
- Look at existing plugins:
    * Galaxy mainline
    * https://github.com/bgruening/galaxytools/tree/master/visualisations
- API is now very extensive, everything is accessible with jQuery!

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

- Visualizations require a different way of thinking: server and client side; downloading files rather than system level access

- Interactivity is what makes visualizations different from static tools

- Requires understanding of both the Galaxy ecosystem as well as HTML5/JS

- Performance is more important than for static Galaxy tools

---

## 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>
		</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/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><a href="/training-material/hall-of-fame/lecorguille/" class="contributor-badge contributor-badge-small contributor-lecorguille"><img src="https://avatars.githubusercontent.com/lecorguille?s=36" alt="Gildas Le Corguillé 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/yhoogstrate/" class="contributor-badge contributor-badge-small contributor-yhoogstrate"><img src="https://avatars.githubusercontent.com/yhoogstrate?s=36" alt="Youri Hoogstrate 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></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/>