/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.charts;
import org.apache.commons.math.stat.StatUtils;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.*;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.collections.DoubleArrayList;
import java.util.*;
/**
* @author Jim Robinson
* @date 10/22/11
*/
public class ScatterPlotUtils {
/**
* Open a plot on an all loaded data
* <p/>
* OTHER, COPY_NUMBER, GENE_EXPRESSION, CHIP, DNA_METHYLATION, TILING_ARRAY, PHASTCON,
* ALLELE_SPECIFIC_COPY_NUMBER, LOH, MUTATION, RNAI, POOLED_RNAI, CHIP_CHIP, CNV,
* ALLELE_FREQUENCY, COVERAGE, REPMASK, EXPR
*/
static HashSet<TrackType> plottableTypes = new HashSet();
public static final String MUTATION_COUNT = "Mutation Count";
static {
plottableTypes.add(TrackType.COPY_NUMBER);
plottableTypes.add(TrackType.GENE_EXPRESSION);
plottableTypes.add(TrackType.DNA_METHYLATION);
}
public static void openPlot(String chr, int start, int end, int zoom) {
ScatterPlotData spData = getScatterPlotData(chr, start, end, zoom);
final ScatterPlotFrame igvPlotFrame = new ScatterPlotFrame(spData);
UIUtilities.invokeOnEventThread(new Runnable() {
public void run() {
igvPlotFrame.setVisible(true);
}
});
}
public static boolean hasPlottableTracks() {
List<Track> tracks = IGV.getInstance().getAllTracks();
for (Track t : tracks) {
if (plottableTypes.contains(t.getTrackType())) {
return true;
}
}
return false;
}
private static ScatterPlotData getScatterPlotData(String chr, int start, int end, int zoom) {
List<Track> tracks = IGV.getInstance().getAllTracks();
List<String> attributeNames = AttributeManager.getInstance().getAttributeNames();
LinkedHashMap<String, SampleData> sampleDataMap = new LinkedHashMap<String, SampleData>();
LinkedHashSet<TrackType> types = new LinkedHashSet<TrackType>();
// Create a map to keep track of the set of all attribute values for each attribute category.
LinkedHashMap<String, Set<String>> uniqueAttributeValues = new LinkedHashMap<String, Set<String>>();
for (String att : attributeNames) {
uniqueAttributeValues.put(att, new HashSet<String>());
}
uniqueAttributeValues.put(MUTATION_COUNT, new HashSet<String>());
HashSet<String> nonSharedAttributes = new HashSet<String>();
//String overlayAttribute = IGV.getInstance().getSession().getOverlayAttribute();
for (Track t : tracks) {
String sample = t.getSample();
TrackType type = t.getTrackType();
if (type == TrackType.MUTATION) {
// Classify sample by mutation count
SampleData sampleData = sampleDataMap.get(sample);
if (sampleData != null) {
int mutCount = getMutationCount(chr, start, end, zoom, t);
String mutCountString = mutCount < 5 ? String.valueOf(mutCount) : "> 5";
sampleData.addAttributeValue(MUTATION_COUNT, mutCountString);
uniqueAttributeValues.get(MUTATION_COUNT).add(mutCountString);
sampleData.setMutationCount(mutCount);
}
} else if (t instanceof DataTrack) {
DataTrack dataTrack = (DataTrack) t;
if (plottableTypes.contains(type)) {
double regionScore = dataTrack.getAverageScore(chr, start, end, zoom);
if (!Double.isNaN(regionScore)) {
types.add(type);
SampleData sampleData = sampleDataMap.get(sample);
if (sampleData == null) {
sampleData = new SampleData();
sampleDataMap.put(sample, sampleData);
}
for (String att : attributeNames) {
final String attributeValue = dataTrack.getAttributeValue(att);
sampleData.addAttributeValue(att, attributeValue);
uniqueAttributeValues.get(att).add(attributeValue);
final String otherValue = sampleData.getAttributesMap().get(att);
if (attributeValue == null) {
if (otherValue != null) {
nonSharedAttributes.add(att);
}
} else if (otherValue == null) {
if (attributeValue != null) {
nonSharedAttributes.add(att);
}
} else {
if (!attributeValue.equals(otherValue)) {
nonSharedAttributes.add(att);
}
}
}
sampleData.addDataValue(type, regionScore);
}
}
}
}
String[] sampleNames = sampleDataMap.keySet().toArray(new String[sampleDataMap.size()]);
// Data
Map<String, double[]> dataMap = new HashMap<String, double[]>(types.size());
// Loop through track (data) types
Map<TrackType, Integer> typeCounts = new HashMap<TrackType, Integer>();
for (TrackType type : types) {
double[] data = new double[sampleNames.length];
for (int i = 0; i < sampleNames.length; i++) {
SampleData sd = sampleDataMap.get(sampleNames[i]);
// Check for null? Should be impossible
double value;
DoubleArrayList valueList = sd.getData(type);
if (valueList == null || valueList.isEmpty()) {
value = Double.NaN;
} else if (valueList.size() == 1) {
int cnt = typeCounts.get(type) == null ? 1 : typeCounts.get(type) + 1;
typeCounts.put(type, cnt);
value = valueList.get(0);
} else {
int cnt = typeCounts.get(type) == null ? valueList.size() : typeCounts.get(type) + valueList.size();
typeCounts.put(type, cnt);
double[] vs = valueList.toArray();
value = StatUtils.mean(vs);
}
data[i] = value;
}
dataMap.put(type.toString(), data);
}
// Attributes
// Get list of "reasonable" attributes with respect to plot series => greater than 1 distinct value, but less
// than 10.
List<String> seriesNames = new ArrayList<String>();
for (Map.Entry<String, Set<String>> entry : uniqueAttributeValues.entrySet()) {
int cnt = entry.getValue().size();
String att = entry.getKey();
if (cnt > 1 && cnt < 10 && !nonSharedAttributes.contains(att) &&
!att.equalsIgnoreCase("DATA FILE") && !(att.equalsIgnoreCase("DATA TYPE"))) {
seriesNames.add(att);
}
}
Map<String, String[]> attMap = new HashMap<String, String[]>(seriesNames.size());
// Loop through attribute types
for (String att : seriesNames) {
String[] attributes = new String[sampleNames.length];
for (int i = 0; i < sampleNames.length; i++) {
SampleData sd = sampleDataMap.get(sampleNames[i]);
// Check for null? Should be impossible
final String s = sd.getAttributesMap().get(att);
attributes[i] = s;
}
attMap.put(att, attributes);
}
// Collect mutation counts
int[] mutationCounts = new int[sampleNames.length];
for (int i = 0; i < sampleNames.length; i++) {
SampleData sd = sampleDataMap.get(sampleNames[i]);
// Check for null? Should be impossible
mutationCounts[i] = sd.getMutationCount();
}
String title = chr + ":" + start + "-" + end;
return new ScatterPlotData(title, sampleNames, attMap, dataMap, mutationCounts);
}
public static int getMutationCount(String chr, int start, int end, int zoom, Track track) {
return (int) track.getRegionScore(chr, start, end, zoom, RegionScoreType.MUTATION_COUNT, FrameManager.getDefaultFrame().getName());
}
/**
* Container for all data and attributes for a single sample
*/
public static class SampleData {
Map<TrackType, DoubleArrayList> valueMap = new HashMap<TrackType, DoubleArrayList>();
Map<String, String> attributesMap = new HashMap<String, String>();
int mutationCount;
public void addDataValue(TrackType type, double value) {
DoubleArrayList valueArray = valueMap.get(type);
if (valueArray == null) {
valueArray = new DoubleArrayList();
valueMap.put(type, valueArray);
}
valueArray.add(value);
}
public DoubleArrayList getData(TrackType type) {
return valueMap.get(type);
}
public void addAttributeValue(String att, String attributeValue) {
attributesMap.put(att, attributeValue);
}
public Map<String, String> getAttributesMap() {
return attributesMap;
}
public void setMutationCount(int mutationCount) {
this.mutationCount = mutationCount;
}
public int getMutationCount() {
return mutationCount;
}
}
}