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| 1 | +/* |
| 2 | + * #%L |
| 3 | + * org.gitools.matrix |
| 4 | + * %% |
| 5 | + * Copyright (C) 2013 - 2016 Universitat Pompeu Fabra - Biomedical Genomics group |
| 6 | + * %% |
| 7 | + * This program is free software: you can redistribute it and/or modify |
| 8 | + * it under the terms of the GNU General Public License as |
| 9 | + * published by the Free Software Foundation, either version 3 of the |
| 10 | + * License, or (at your option) any later version. |
| 11 | + * |
| 12 | + * This program is distributed in the hope that it will be useful, |
| 13 | + * but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 14 | + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 15 | + * GNU General Public License for more details. |
| 16 | + * |
| 17 | + * You should have received a copy of the GNU General Public |
| 18 | + * License along with this program. If not, see |
| 19 | + * <http://www.gnu.org/licenses/gpl-3.0.html>. |
| 20 | + * #L% |
| 21 | + */ |
| 22 | +package org.gitools.matrix.transform; |
| 23 | + |
| 24 | +import org.gitools.api.ApplicationContext; |
| 25 | +import org.gitools.api.analysis.IAggregator; |
| 26 | +import org.gitools.api.analysis.IProgressMonitor; |
| 27 | +import org.gitools.api.matrix.*; |
| 28 | +import org.gitools.matrix.model.MatrixLayer; |
| 29 | +import org.gitools.matrix.transform.parameters.AggregatorParameter; |
| 30 | +import org.gitools.utils.aggregation.MeanAggregator; |
| 31 | +import org.gitools.utils.aggregation.MedianAggregator; |
| 32 | +import org.gitools.utils.aggregation.StdDevAggregator; |
| 33 | + |
| 34 | + |
| 35 | +public class ZScoreFunction extends ConfigurableTransformFunction { |
| 36 | + |
| 37 | + public static final String AGGREGATION_PARAM = "Aggregation"; |
| 38 | + AggregatorParameter aggregatorParameter; |
| 39 | + |
| 40 | + private IProgressMonitor monitor; |
| 41 | + private Double estimator; |
| 42 | + private Double stdDev; |
| 43 | + |
| 44 | + |
| 45 | + public ZScoreFunction() { |
| 46 | + super("Fold-Change"); |
| 47 | + } |
| 48 | + |
| 49 | + |
| 50 | + @Override |
| 51 | + public Double apply(Double value, IMatrixPosition position) { |
| 52 | + |
| 53 | + if (estimator == null || stdDev == null || value == null) { |
| 54 | + return null; |
| 55 | + } else { |
| 56 | + return (value - estimator) / stdDev; |
| 57 | + } |
| 58 | + |
| 59 | + } |
| 60 | + |
| 61 | + |
| 62 | + @Override |
| 63 | + public void onBeforeIterate(IMatrixIterable<Double> parentIterable) { |
| 64 | + super.onBeforeIterate(parentIterable); |
| 65 | + monitor = ApplicationContext.getProgressMonitor().subtask(); |
| 66 | + |
| 67 | + |
| 68 | + IMatrix matrix = parentIterable.getPosition().getMatrix(); |
| 69 | + |
| 70 | + IMatrixLayer aggLayer = new MatrixLayer("agg", Double.class); |
| 71 | + |
| 72 | + estimator = aggregatorParameter.getParameterValue().aggregate(parentIterable); |
| 73 | + stdDev = StdDevAggregator.INSTANCE.aggregate(parentIterable); |
| 74 | + |
| 75 | + monitor.end(); |
| 76 | + } |
| 77 | + |
| 78 | + |
| 79 | + |
| 80 | + @Override |
| 81 | + public ZScoreFunction createNew() { |
| 82 | + return new ZScoreFunction(); |
| 83 | + } |
| 84 | + |
| 85 | + @Override |
| 86 | + protected void createDefaultParameters() { |
| 87 | + aggregatorParameter = new AggregatorParameter(); |
| 88 | + aggregatorParameter.setDescription("Select if the fold change should be calculated with the row/column median or mean"); |
| 89 | + IAggregator[] iAggregators = { |
| 90 | + MedianAggregator.INSTANCE, |
| 91 | + MeanAggregator.INSTANCE |
| 92 | + }; |
| 93 | + aggregatorParameter.setChoices(iAggregators); |
| 94 | + addParameter(AGGREGATION_PARAM, aggregatorParameter); |
| 95 | + |
| 96 | + } |
| 97 | + |
| 98 | + public String getName() { |
| 99 | + return "Z-score"; |
| 100 | + } |
| 101 | + |
| 102 | + public String getDescription() { |
| 103 | + return "The Z-score reflects the relationship to the estimator of all values"; |
| 104 | + } |
| 105 | + |
| 106 | +} |
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