Fireworks Exporter

Exports the pathways overview as raster images.

Introduction

The fireworks project aims to provide 'a genome-wide, hierarchical visualisation of Reactome pathways in a space-filling graph'. The fireworks exporter allows to generate these views in png, jpg or gif and download them into your computer.

Install

Fireworks exporter can be included into your project using maven. Add the dependency:

 <dependencies>
    <dependency>
        <groupId>org.reactome.server.tools</groupId>
        <artifactId>fireworks-exporter</artifactId>
        <version>1.0.0</version>
    </dependency>
</dependencies>

and the EBI repository:

<repositories>
    <repository>
        <id>nexus-ebi-repo-release</id>
        <name>The EBI internal repository</name>
        <url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
    </repository>

</repositories>

Usage

Resources

fireworks exporter needs access to the json files describing the layout of each species. This files can be found at https://reactome.org/download/current/fireworks/.

Exporting a fireworks

A basic fireworks can be created with a few lines of codes.

String fireworks_path = "path/to/fireworks";
FireworkArgs args = new FireworkArgs("Homo_sapiens", "png");
FireworksExporter exporter = new FireworksExporter(args, fireworks_path);
BufferedImage image = exporter.render();

To save the image to a file, use the java ImageIO.write() method.

File file = new File("images", "Homo_sapiens.png");
ImageIO.write(image, "png", file);

If you want to see some pathways selected into the fireworks, you can specify its stable identifier (stId) or database identifier (dbId). We can also increase the resolution of the image.

String fireworks_path = "path/to/fireworks";
FireworkArgs args = new FireworkArgs("Homo_sapiens", "png");

args.setSelected(Arrays.asList("R-HSA-169911", "R-HSA-3560792"));
args.setFactor(5.0);

FireworksExporter exporter = new FireworksExporter(args, fireworks_path);
BufferedImage image = exporter.render();

Now the pathways (and all of their top level pathways) are highlighted in a different color.

You can also locate a particular molecule using the flag system. The flags allow you to show in a different color the pathways where a molecule (or a set of molecules) is present.

String fireworks_path = "path/to/fireworks";
FireworkArgs args = new FireworkArgs("Homo_sapiens", "png");
args.setFactor(5.0);

// Flagging is a reactome service.
ContentServiceClient.setHost("https://reactome.org/");
args.setFlags(Arrays.asList("CTP");

FireworksExporter exporter = new FireworksExporter(args, fireworks_path);
BufferedImage image = exporter.render();

What if I want a more complex analysis of data? Reactome provides an analysis service that allows to send your data and visualize it on top of the diagram. To see more about how to perform an analysis go to https://reactome.org/dev/analysis.

Once you have performed the analysis, you only need to specify the token and the reactome server.

String fireworks_path = "path/to/fireworks";
FireworkArgs args = new FireworkArgs("Homo_sapiens", "png");
args.setFactor(5.0);

// Analysis tokens get invalidated after a while
// Be sure to perform the analysis before copying the token.
AnalysisClient.setServer("https://reactome.org");
args.setToken("MjAxNzExMzAwOTI3MTBfMTM%253D");

FireworksExporter exporter = new FireworksExporter(args, fireworks_path);
BufferedImage image = exporter.render();

You can change the color style if you find it more comfortable. We provide 4 different color profiles: Copper, Copper plus, Barium Lithium and Calcium Salts.

String fireworks_path = "path/to/fireworks";
FireworkArgs args = new FireworkArgs("Homo_sapiens", "png");
args.setFactor(5.0);
AnalysisClient.setServer("https://reactome.org");
args.setToken("MjAxNzExMzAwOTI3MTBfMTM%253D");

args.setProfile("Barium Lithium");

FireworksExporter exporter = new FireworksExporter(args, fireworks_path);
BufferedImage image = exporter.render();

Sometimes, an analysis contains time series. To visualise them, images can be exported as animated GIF. This option is only supported with gif format.

FireworkArgs args = new FireworkArgs("Homo_sapiens", "gif");
args.setSelected(Arrays.asList("R-HSA-169911", "R-HSA-3560792"));
args.setProfile("Copper plus");
AnalysisClient.setServer("https://reactome.org");
args.setToken("MjAxNzExMzAwOTI3MTBfMTM%253D");
FireworksExporter exporter = new FireworksExporter(args, fireworks_path);

File file = new File("images", "Homo_sapiens.gif");
FileOutputStream outputStream = new FileOutputStream(file);
exporter.renderToGif(outputStream);