Visualisations in Galaxy

name: inverse
layout: true
class: center, middle, inverse

</span></div>

</span></div>

---

# Visualisations in Galaxy

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

</div>

<div class="footnote" style="bottom: 8em;">
  <i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated:   
  <i class="fas fa-fingerprint" aria-hidden="true"></i><span class="visually-hidden">purl</span><abbr title="Persistent URL">PURL</abbr>: <a href="https://gxy.io/GTN:S00101">gxy.io/GTN:S00101</a>
</div>

<div class="footnote" style="bottom: 5em;">

<i class="fas fa-file-alt" aria-hidden="true"></i><span class="visually-hidden">text-document</span><a href="slides-plain.html"> Plain-text slides</a> |

</div>

<div class="footnote" style="bottom: 2em;">
    <strong>Tip: </strong>press <kbd>P</kbd> to view the presenter notes
    | <i class="fa fa-arrows" aria-hidden="true"></i><span class="visually-hidden">arrow-keys</span> Use arrow keys to move between slides

</div>

???
Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

Press `P` again to switch presenter notes off

Press `C` to create a new window where the same presentation will be displayed.
This window is linked to the main window. Changing slides on one will cause the
slide to change on the other.

Useful when presenting.

---

# 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)

---

# 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)

---

## 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.

---

## Data Visualisation in Galaxy

---

## Genome Browsers

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

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

---

## 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)

---

## 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

---

## 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)]

---

## 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)

---

## 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)

---

## Visualisation Tools

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

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

---

## Related tutorials

---

## 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!

<div class="contributors-line">
		Authors: <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>
	</div>

</div>

</div>

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/>