Package org.monarchinitiative.lirical.io.output.svg

Class Lr2Svg

java.lang.Object

org.monarchinitiative.lirical.io.output.svg.Lirical2Svg

org.monarchinitiative.lirical.io.output.svg.Lr2Svg

public class Lr2Svg
extends Lirical2Svg

This class creates an SVG file representing the results of likelihood ratio analysis of an HPO case.

Author:

Peter Robinson

Field Summary

Fields inherited from class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg

BLACK, BLUE, BOX_HEIGHT, BOX_OFFSET, BRIGHT_GREEN, BROWN, DARKBLUE, GREEN, MIN_VERTICAL_OFFSET, ORANGE, RED, VIOLET

Constructor Summary

Constructors

Constructor	Description
Lr2Svg(TestResult result, int rank, org.monarchinitiative.phenol.ontology.data.TermId diseaseId, String originalDiseaseName, org.monarchinitiative.phenol.ontology.data.MinimalOntology hpo, String symbol)	Constructor to draw an SVG representation of the phenotype and genotype likelihood ratios

Method Summary

Modifier and Type	Method	Description
String	getSvgString()
int	rank()
void	writeSvg(String path)

Methods inherited from class org.monarchinitiative.lirical.io.output.svg.Lirical2Svg

prettifyDiseaseName, sortByValue, writeDiamond, writeDiamond, writeFooter

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Lr2Svg

public Lr2Svg(TestResult result,
 int rank,
 org.monarchinitiative.phenol.ontology.data.TermId diseaseId,
 String originalDiseaseName,
 org.monarchinitiative.phenol.ontology.data.MinimalOntology hpo,
 String symbol)

Constructor to draw an SVG representation of the phenotype and genotype likelihood ratios

Parameters:

result - The test result

rank -

diseaseId - The current differential diagnosis id (e.g., OMIM:600123)

originalDiseaseName - The current differential diagnosis name

hpo - Reference to HPO ontology

symbol - Gene symbol (if any, can be null)

Method Details

getSvgString

public String getSvgString()

writeSvg

public void writeSvg(String path)

rank

public int rank()