name: inverse layout: true class: center, middle, inverse <div class="my-header"><span> <a href="/training-material/topics/visualisation" title="Return to topic page" ><i class="fa fa-level-up" aria-hidden="true"></i></a> <a class="nav-link" href="https://github.com/galaxyproject/training-material/edit/main/topics/visualisation/tutorials/introduction/slides.html"><i class="fa fa-pencil" aria-hidden="true"></i></a> </span></div> <div class="my-footer"><span> <img src="/training-material/assets/images/GTN-60px.png" alt="Galaxy Training Network" style="height: 40px;"/> </span></div> --- <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" class="cover-logo"/> # Visualisations in Galaxy <div markdown="0"> <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"/><img src="https://avatars.githubusercontent.com/hexylena?s=27" alt="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"/><img src="https://avatars.githubusercontent.com/shiltemann?s=27" alt="Avatar">Saskia Hiltemann</a> </div> </div> <!-- modified date --> <div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: </div> <!-- other slide formats (video and plain-text) --> <div class="footnote" style="bottom: 6em;"> <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> <!-- usage tips --> <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> ??? 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Useful when presenting. --- ## Requirements Before diving into this slide deck, we recommend you to have a look at: - [Introduction to Galaxy Analyses](/training-material/topics/introduction) --- # What is Data Visualisation - Making graphics to clearly convey data - Many different options  --- # What is Data Visualisation - More than just scatter plots and bar charts - Many domain-specific - Protein folding, network graphs, trees, genome browsers  --- ## 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[] ] ??? 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, ..  --- ## Genome Browsers in Galaxy - As display applications - e.g. UCSC browser, IBV, IGB, .. - accessed via links on dataset  --- ## JBrowse - Genome browser as a regular tool - Configure your settings .image-75[  ] ??? - JBrowse is not a display application like the previous examples - Regular Galaxy tool --- ## JBrowse - Then interactively explore your genome .image-75[] --- ## Galaxy Charts - Accessed through Charts icon <i class="fas fa-chart-bar" aria-hidden="true"></i><span class="visually-hidden">galaxy-barchart</span> on dataset - Different options depending on datatype  --- ## Galaxy Charts - After selecting chart type, can customize settings - Example: Protein Viewer  --- ## Visualisation Tools - Many tools for visualisation - Example: Circos for circular data plots  --- ## 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 markdown="0"> <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"/><img src="https://avatars.githubusercontent.com/hexylena?s=27" alt="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"/><img src="https://avatars.githubusercontent.com/shiltemann?s=27" alt="Avatar">Saskia Hiltemann</a> </div> </div> <div style="display: flex;flex-direction: row;align-items: center;justify-content: center;"> <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" style="height: 100px;"/> </div> <a rel="license" href="https://creativecommons.org/licenses/by/4.0/"> This material is licensed under the Creative Commons Attribution 4.0 International License</a>.