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# Generic plugins
Saskia Hiltemann
Youri Hoogstrate
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Useful when presenting. --- ## 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 --- ## 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!
Authors:
Saskia Hiltemann
Youri Hoogstrate
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