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

Class Sparkline2Svg

java.lang.Object

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

org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg

public class Sparkline2Svg
extends Lirical2Svg

Make a set of sparklines for the top of the page. Note that in the "main" HPO/Gene plots for each disease, each of the the features orders the HPO according to the individual likelihood ratios, but for the sparklines we want to have the same order for each 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
Sparkline2Svg(TestResult result, boolean useGenotype, org.monarchinitiative.phenol.ontology.data.MinimalOntology ontology)	Set up the Sparkline2Svg generator by sorting the HPO terms according to their likelihood ratios in the top diagnosis (diseaseId).

Method Summary

Modifier and Type	Method	Description
String	getGeneSparklineSvg(AnalysisResults results, org.monarchinitiative.phenol.ontology.data.TermId diseaseId, String gsymbol)
String	getPosttestBar(double ptprob)
String	getSparklineSvg(String gsymbol, TestResult result)
String	getSparklineSvg(TestResult result)	This is used by Phenotype only output.

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

Sparkline2Svg

public Sparkline2Svg(TestResult result,
 boolean useGenotype,
 org.monarchinitiative.phenol.ontology.data.MinimalOntology ontology)

Set up the Sparkline2Svg generator by sorting the HPO terms according to their likelihood ratios in the top diagnosis (diseaseId).

Parameters:

result - A representation of the Case

Method Details

getSparklineSvg

public String getSparklineSvg(TestResult result)

This is used by Phenotype only output. We supply an empty string instead of a gene symbol. Note that because the test results know that they do not have a genotype, this will not affect the output.

Parameters:

result - test result

Returns:

an SVG string

getSparklineSvg

public String getSparklineSvg(String gsymbol,
 TestResult result)

getGeneSparklineSvg

public String getGeneSparklineSvg(AnalysisResults results,
 org.monarchinitiative.phenol.ontology.data.TermId diseaseId,
 String gsymbol)

getPosttestBar

public String getPosttestBar(double ptprob)