Analysis Report

Creates a PDF document with a report of an analysis performed in Reactome. Click here to know more about Analysis Service.

The resulting PDF will contain the minimum information to reproduce the analysis, as well as details for the most relevant pathways, sorted by p-value.

Installation

Analysis exporter is developed as a Java library. To add it to your project, you have to use maven:

<dependencies>
	<dependency>
		<groupId>org.reactome.server.tools</groupId>
		<artifactId>analysis-report</artifactId>
		<version>1.1.1</version>
	</dependency>
	<!-- ... -->
</dependencies>
<repositories>
	<repository>
		<id>pst-release</id>
		<name>EBI Nexus Repository</name>
		<url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
	</repository>
	<!-- ... -->
<repositories>

Usage

This project needs a connection to the grap database (see graph-core).

PDFs are generated by an instance of the ReportBuilder class.

// Configure Reactome graph database
ReactomeGraphCore.initialise("host", "port", "username", "password", Neo4jConfig.class);

AnalysisReport builder = new AnalysisReport(
	EHLD_PATH,       // EHLD (R-HSA-123.svg) files
	DIAGRAM_PATH,    // layout (12345.json) and graph (12345.grap.json) files.
	ANALYSIS_PATH,   // Analysis (res_20210101_1.bin)
	FIREWORKS_PATH,  // Fireworks (Homo_sapiens.json) files
	SVG_SUMMARY);    // svgsummary.txt

OutputStream os = new FileOutputStream(new File("output.pdf"));
AnalysisStoredResult result = new TokenUtils(ANALYSIS_PATH).getFromToken(token);
builder.create(result, "TOTAL", 48887L, numberOfPathways, "modern", "copper plus", "copper", os);

The parameters of the create method are:

Name	Description
analysis	the analysis results
resource	resource to filter results (default: TOTAL)
species	dbId of the species to filter results (default: 48887L)
maxPathways	max number of pathways to show (default: 25)
diagramProfile	standard or modern (default: modern)
analysisProfile	standard, copper plus, strosobar (default: standard)
fireworksProfile	copper, copper plus, barium lithium or calcium salts (default: copper)
os	output stream

Structure of the PDF

1. Introduction: short text about Reactome and Analysis service.
2. Properties of analysis: properties that characterize the analysis.
   • Analysis type
   • Pathways found
   • Identifiers found
   • Projected to human
   • Include interactors
   • Pathways species
   • unique ID of the analysis
3. Genome-wide overview: pathway overview with the analysis overlaid.
4. Most significant pathways table: table with the maxPathways most significant pathways filtered by resource and species and sorted by FDR.
   • name
   • found entities
   • entities ratio
   • p-value and FDR
   • found reactions
   • reactions ratio
5. Most significant pathways details: each of the most significaint pathways is layout in a new page. For each of them, we show:
   • diagram
   • diseases, compartments, inferences
   • summation
   • edit history
   • elements found
6. Foud identifiers: List of input identifiers found with their corresponding mapping. If the analysis is an expression analysis, more columns are added to show time series.
7. Not foud identifiers: list of input identifiers not found.