ubic.BAMSandAllen.FocusedAnalysis.TestConnectivityRobustness.java Source code

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Here is the source code for ubic.BAMSandAllen.FocusedAnalysis.TestConnectivityRobustness.java

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/*******************************************************************************
 * The ABAMS project
 * 
 * Copyright (c) 2012 University of British Columbia
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *       http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 ******************************************************************************/
package ubic.BAMSandAllen.FocusedAnalysis;

import java.util.LinkedList;
import java.util.List;
import java.util.Random;

import javax.media.j3d.Link;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import ubic.BAMSandAllen.AnalyzeBAMSandAllenGenes;
import ubic.BAMSandAllen.RankedGeneListLoader;
import ubic.BAMSandAllen.AnalyzeBAMSandAllenGenes.Direction;
import ubic.BAMSandAllen.MatrixPairs.ConnectivityAndAllenExpressionMatrixPair;
import ubic.BAMSandAllen.MatrixPairs.ExpressionMatrixPairFactory;
import ubic.BAMSandAllen.MatrixPairs.MatrixPair;
import ubic.BAMSandAllen.MatrixPairs.ConnectivityAndAllenPartialExpressionMatrixPair.RegressMatrix;

public class TestConnectivityRobustness {
    private static Log log = LogFactory.getLog(MatrixPair.class.getName());

    /**
     * @param args
     */
    public static void main(String[] args) throws Exception {

        main2();
        System.exit(1);

        Direction direction = AnalyzeBAMSandAllenGenes.Direction.OUTGOING;
        boolean makeVirtualRegions = true;

        boolean squareMatrix = false;
        boolean logDistance = true;
        boolean slow = false;
        RegressMatrix regressType = RegressMatrix.BOTH;
        boolean useVirtual = true;
        boolean removeNonExp = true;

        ConnectivityAndAllenExpressionMatrixPair pair = ExpressionMatrixPairFactory.connectivityPartial(direction,
                slow, regressType, useVirtual, removeNonExp, logDistance);
        pair.getCorrelation();
        // ConnectivityAndAllenExpressionMatrixPair pair = ExpressionMatrixPairFactory.connectivityAndExpression(
        // direction, useVirtual, removeNonExp );

        String filename = "/grp/java/workspace/BAMSandAllen/data/rankedGenes/near final ammon/";
        filename += "LOOGenesInOrder.in.partialcon.ammon.txt.452.0.01985.topGenes.txt";
        // filename += "LOOGenesInOrder.out.partialcon.ammon.txt.374.0.016424.topGenes.txt";

        RankedGeneListLoader aLook = new RankedGeneListLoader(filename);
        pair.setMatrixBDataRows(aLook.getLines());
        log.info("Original:" + pair.getCorrelation());

        log.info(pair.runJackKnife(true));

        // second try

        List<String> connectionRows = pair.getMatrixA().getRowNames();
        int seed = 7;
        Random r = new Random(seed);
        List<String> removeRows = new LinkedList<String>();
        for (String region : connectionRows) {
            boolean remove = r.nextBoolean();
            if (remove) {
                removeRows.add(region);
            }
        }
        pair.removeMatrixADataRows(removeRows);
        pair.printConnectionInfo();
        pair.printDimensions();
        log.info("After remvoing half:" + pair.getCorrelation() + ", seed=" + seed);

    }

    public static void main2() throws Exception {
        Direction direction = AnalyzeBAMSandAllenGenes.Direction.INCOMING;
        boolean makeVirtualRegions = true;

        boolean squareMatrix = false;
        boolean logDistance = true;
        boolean slow = false;
        RegressMatrix regressType = RegressMatrix.BOTH;
        boolean useVirtual = true;
        boolean removeNonExp = true;
        boolean run = false;

        List<Double> resultCor = new LinkedList<Double>();
        List<Double> resultSig = new LinkedList<Double>();

        int seed = 1;
        int splits = 2;

        for (int i = 0; i < splits; i++) {
            ConnectivityAndAllenExpressionMatrixPair pair = ExpressionMatrixPairFactory.connectivityPartial(
                    direction, slow, regressType, useVirtual, removeNonExp, logDistance, squareMatrix, run);

            pair.removeZeroConnectionRows();

            //            String filename = "/grp/java/workspace/BAMSandAllen/data/rankedGenes/near final ammon/";
            //             filename += "LOOGenesInOrder.in.partialcon.ammon.txt.452.0.01985.topGenes.txt";
            //            //filename += "LOOGenesInOrder.out.partialcon.ammon.txt.374.0.016424.topGenes.txt";
            //            RankedGeneListLoader aLook = new RankedGeneListLoader( filename );
            //            pair.setMatrixBDataRows( aLook.getLines() );

            // remove rows
            List<String> connectionRows = pair.getMatrixA().getRowNames();
            List<String> removeRows = new LinkedList<String>();
            Random r = new Random(seed);
            for (String region : connectionRows) {
                int remove = (int) (r.nextDouble() * splits);
                if (remove != i) {
                    removeRows.add(region);
                }
            }
            pair.removeMatrixADataRows(removeRows);
            pair.printConnectionInfo();
            pair.printDimensions();
            pair.run();
            double correlation = pair.getCorrelation();
            log.info(correlation);
            resultCor.add(correlation);
            resultSig.add(pair.test(1000));
        }
        log.info("Correlations:" + resultCor);
        log.info("Pvalues:" + resultSig);
    }
}