Class HeatmapStandardize

  • All Implemented Interfaces:
    adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<>, adams.core.SizeOfHandler,<Heatmap>, Serializable, Comparable

    public class HeatmapStandardize
    Standardizes the values of a heatmap to have mean of 1 and stdev 1.
    NB: normally, the mean is 0 when standardizing, but heatmaps only allow positive values.

    Valid options are:

    -D <int> (property: debugLevel)
        The greater the number the more additional info the scheme may output to
        the console (0 = off).
        default: 0
        minimum: 0
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form
    • Nested Class Summary

      • Nested classes/interfaces inherited from class<T extends>
    • Field Summary

      Modifier and Type Field Description
      protected boolean m_IsSample
      whether the arrays are samples or populations.
      • Fields inherited from class

      • Fields inherited from class adams.core.option.AbstractOptionHandler

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      String globalInfo()
      Returns a string describing the object.
      protected Heatmap processData​(Heatmap data)
      Performs the actual filtering.
      • Methods inherited from class

        checkData, cleanUp, compareTo, defineOptions, destroy, dontUpdateIDTipText, equals, filter, forCommandLine, getDontUpdateID, reset, setDontUpdateID, shallowCopy, shallowCopy
      • Methods inherited from class adams.core.option.AbstractOptionHandler

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, initialize, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString
      • Methods inherited from class adams.core.logging.LoggingObject

        configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf
      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel, setLoggingLevel
      • Methods inherited from interface adams.core.logging.LoggingSupporter

        getLogger, isLoggingEnabled
      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager, toCommandLine
    • Field Detail

      • m_IsSample

        protected boolean m_IsSample
        whether the arrays are samples or populations.
    • Constructor Detail

      • HeatmapStandardize

        public HeatmapStandardize()
    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        a description suitable for displaying in the gui
      • processData

        protected Heatmap processData​(Heatmap data)
        Performs the actual filtering.
        Specified by:
        processData in class<Heatmap>
        data - the data to filter
        the filtered data