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Merge branch 'refactor'
* refactor: Finished refactoring GWASGeneViewer
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‎.gitignore

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target/
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*.class
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# Package Files #
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*.jar
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*.war
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# gwt caches and compiled units #
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war/gwt_bree/
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gwt-unitCache/
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# boilerplate generated classes #
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.apt_generated/
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# more caches and things from deploy #
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war/WEB-INF/deploy/
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war/WEB-INF/classes/

‎README

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‎README.md

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## What is GWASViewer?
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GWASViewer is a Google Web Toolkit (GWT) widget for displaying interactive Manhattan plots.
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It is a composite of multiple different GWT widgets:
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1. [dygraphs-gwt][0] as the actual Manhattan plot and statistic plots
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2. [GeneViewer][1] as the gene annotation track
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3. [LDViewer][2] as a LD triangle viewer
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![GWASViewer](https://raw.githubusercontent.com/timeu/GeneViewer/master/gwasviewer.png "GWASViewer")
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## How do I use it?
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Following minimum steps are required:
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```JAVA
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// create a GeneDataSource for the `GeneViewer` to dynamically fetch genes
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final GeneDataSource geneDataSource = new GeneDataSource() {
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@Override
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public void fetchGenes(String chr, int start, int end, boolean getFeatures, FetchGenesCallback callback) {
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// fetch the genes for the provided region from the backend for example
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}
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@Override
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public void fetchGeneInfo(String name, FetchGeneInfoCallback callback) {
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// fetch the gene info/description for the specific gene name
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}
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};
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// the default color of the Manhattan plot is blue and the marked regions are green
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GWASViewer viewer = new GWASViewer("Chr1",new String[]{"blue"},"green",geneDataSource);
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// draw the manhattan plot
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viewer.draw(dataTable, maxScore, fdrThreshold, chrLengths);
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```
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### Load list of tracks and handle the track selection
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`GWASViewer` can display a list of tracks when the user opens the settings popup.
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The user can set this list by using the `setTracks` function:
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```
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Tracks[] listOfTracks = // get from server for example
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viewer.setTracks(listOfTracks);
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```
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When the user selects a track from the popup, an `SelectTrackEvent` event will be fired. The user can handle the event
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retrieve the data from the backend and then call `setTrackData` to display the track:
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```
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viewer.addHandler(new SelectTrackEvent.Handler() {
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@Override
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public void onSelectTrack(SelectTrackEvent event) {
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DataTable dataTable = //get track data from backend for example
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viewer.setTrackData(event.getId(),event.isStacked(),dataTable);
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}
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},SelectTrackEvent.getType());
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The track data has to be provided as a [gwt-charts][3] DataTable object with 2 columns (position, and value).
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### Display LD Triangle plot or LD colored values
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To display the LD triangle plot use the `loadLDPlot` function and for coloring the Manhattan plots based on LD
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the user can use `showColoredLDValues`. For more information refer to the [LDViewer documentation][2].
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### Highlight region and select SNPs
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To highlight one or multiple regions, use the `addDisplayFeature` function and to clear it use `clearDisplayFeatures()`:
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```
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viewer.addDisplayFeature(new DisplayFeature("AT4G00651.1", 271486, 271879, "red"), true);
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viewer.addDisplayFeature(new DisplayFeature("Some interesting region", 8753993, 9241760, "green"), true);
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```
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To select one or more SNPs use `setSelections` and to clear `clearSelections()`:
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```
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selections.add(148);
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selections.add(1220);
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selections.add(2240);
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// false will redraw after SNPs are select. If it is set to true, use viewer.refresh() to update the plot
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viewer.setSelections(selections,false);
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```
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### Uploading tracks and custom TrackUploadWidget
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By default the `DefaultTrackUploadWidget` is displayed. It supports uploading to a backend or to the local storage.
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The upload url can be changed with `setDefaultTrackUploadUrl`. The file has to be a comma separated file that can be either
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provided by URL or by selecting it with the a file input.
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When the user uploads a track the `UploadTrackEvent` is fired.
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To implement a custom upload widget, create a `Composite` that implements the `UploadTrackWidget` marker interface
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and use the `setUploadTrackWidget`. To disable the upload functionality call the function with `null`.
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## Useful events:
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See the sample app below for an example how to use those events
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| Event | When fired ? | Parameters | Component |
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|------ | ------------- |-----------| ------------|
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| ClickGeneEvent | When the user clicks on a gene in the gene annotation track | `Gene` instance | `GeneViewer`|
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| HighlightGeneEvent | When the user moves the mouse over a gene in the gene annotation track | `Gene` instance | `GeneViewer` |
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| UnhighlightGeneEvent | When the user moved out of a gene in the gene annotation track | - | `GeneViewer` |
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| ZoomChangeEvent | When the user changes the zoom level of the Manhattan plot | start and end | `GWASViewer` |
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| HighlightPointEvent | When the user highlights a point in the Manhattan plot | x, Point[], row, seriesName | `GWASViewer` |
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| ClickPointEvent | When the user clicks on a point in the Manhattan plot | x, Point[] | `GWASViewer` |
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| SelectTrackEvent | When the user selects a track from the settings popup | id | `GWASViewer` |
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| UploadTrackEvent | When the user uploads a custom track | - | `GWASViewer` |
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| DeleteTrackEvent | When the user deletes a custom track | id | `GWASViewer` |
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## How do I install it?
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If you're using Maven, you can add the following to your `<dependencies>`
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section:
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```xml
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<dependency>
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<groupId>com.github.timeu.gwtlibs.gwasviewer</groupId>
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<artifactId>gwasviewer</artifactId>
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<version>1.0.0</version>
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</dependency>
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```
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GeneViewer uses [GWT 2.8's][4] new [JSInterop feature][5] and thus it has to be enabled in the GWT compiler args.
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For maven:
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```xml
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<compilerArgs>
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<compilerArg>-generateJsInteropExports</compilerArg>
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</compilerArgs>
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```
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or passing it to the compiler via `-generateJsInteropExports`
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You can also download the [jar][6] directly or check out the source using git
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from <https://github.com/timeu/geneviewer.git> and build it yourself. Once
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you've installed LDViewer, be sure to inherit the module in your .gwt.xml
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file like this:
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```xml
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<inherits name='com.github.timeu.gwtlibs.gwasviewer.GWASViewer'/>
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```
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## Where can I learn more?
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* Check out the [sample app][7] ([Source Code][8]) for a full example of using GeneViewer.
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[0]: http://gitub.com/timeu/dygraphs-gwt
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[1]: http://github.com/timeu/GeneViewer
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[2]: http://github.com/timeu/LDViewer
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[3]: https://github.com/google/gwt-charts
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[4]: http://www.gwtproject.org/release-notes.html#Release_Notes_2_8_0_BETA1
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[5]: https://docs.google.com/document/d/10fmlEYIHcyead_4R1S5wKGs1t2I7Fnp_PaNaa7XTEk0/edit#heading=h.o7amqk9edhb9
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[6]: https://github.com/timeu/GWASViewer/releases
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[7]: http://timeu.github.io/GWASViewer
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[8]: https://github.com/timeu/GeneViewer/tree/master/gwasviewer-sample

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