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--- # Visualisations in Galaxy --- ## Requirements Before diving into this slide deck, we recommend you to have a look at: - [Introduction to Galaxy Analyses](/archive/2020-12-01/topics/introduction) .footnote[Tip: press `P` to view the presenter notes] ??? 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 !(../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 !(../../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[!(../../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[ !(../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[![JBrowse screenshot](../images/jbrowse/sequencing.png)] --- ## 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 ![Example of list of Galaxy charts](../images/charts_list.png) --- ## Galaxy Charts - After selecting chart type, can customize settings - Example: Protein Viewer !(../../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://wiki.galaxyproject.org/Teach/GTN) and all the contributors!
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