Examples of org.broadinstitute.gatk.utils.R.RScriptExecutor.exec()

Class org.broadinstitute.gatk.utils.R.RScriptExecutor

Examples of org.broadinstitute.gatk.utils.R.RScriptExecutor.exec()

org.broadinstitute.gatk.utils.R.RScriptExecutor.exec()

            RScriptExecutor executor = new RScriptExecutor();
            executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class));
            executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV);
            // Print out the command line to make it clear to the user what is being executed and how one might modify it
            logger.info("Executing: " + executor.getApproximateCommandLine());
            executor.exec();
        }
    }


    private void createVisualizationScript( final List<VariantDatum> randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff, final String[] annotationKeys ) {
        PrintStream stream;

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        // Execute Rscript command to generate the clustering plots
        RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(RSCRIPT_FILE);
        logger.info("Executing: " + executor.getApproximateCommandLine());
        executor.exec();
     }


    // The Arrange function is how we place the 4 model plots on one page
    // from http://gettinggeneticsdone.blogspot.com/2010/03/arrange-multiple-ggplot2-plots-in-same.html
    private void createArrangeFunction( final PrintStream stream ) {

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        executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class));
        executor.addArgs(csvFile.getAbsolutePath());
        executor.addArgs(exampleReportFile.getAbsolutePath());
        executor.addArgs(output.getAbsolutePath());
        Logger.getLogger(RecalUtils.class).debug("R command line: " + executor.getApproximateCommandLine());
        executor.exec();
    }


    private static void outputRecalibrationPlot(final File csvFile, final RecalibrationArgumentCollection RAC) {


        final RScriptExecutor executor = new RScriptExecutor();

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        final RScriptExecutor executor = new RScriptExecutor();
        executor.addScript(new Resource(SCRIPT_FILE, RecalUtils.class));
        executor.addArgs(csvFile.getAbsolutePath());
        executor.addArgs(RAC.RECAL_TABLE_FILE.getAbsolutePath());
        executor.exec();
    }


    /**
     * Please use {@link #generateCsv(java.io.File, java.util.Map)} and {@link #generatePlots(java.io.File, java.io.File, java.io.File)} instead.
     *

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