Uses of Class
de.jstacs.utils.REnvironment

Packages that use REnvironment

Package	Description
de.jstacs.classifiers	This package provides the framework for any classifier.
de.jstacs.classifiers.utils	Provides some useful classes for working with classifiers.
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous	This package contains various inhomogeneous models.

Uses of REnvironment in de.jstacs.classifiers

Methods in de.jstacs.classifiers with parameters of type REnvironment

Modifier and Type	Method and Description
static StringBuffer	AbstractScoreBasedClassifier.DoubleTableResult.getPlotCommands(REnvironment e, String plotOptions, AbstractScoreBasedClassifier.DoubleTableResult... dtr) This method copies the data to the server side and creates a StringBuffer containing the plot commands.
static StringBuffer	AbstractScoreBasedClassifier.DoubleTableResult.getPlotCommands(REnvironment e, String plotOptions, int[] colors, AbstractScoreBasedClassifier.DoubleTableResult... dtr) This method copies the data to the server side and creates a StringBuffer containing the plot commands.
static StringBuffer	AbstractScoreBasedClassifier.DoubleTableResult.getPlotCommands(REnvironment e, String plotOptions, String[] colors, AbstractScoreBasedClassifier.DoubleTableResult... dtr) This method copies the data to the server side and creates a StringBuffer containing the plot commands.
static ImageResult	AbstractScoreBasedClassifier.DoubleTableResult.plot(REnvironment e, AbstractScoreBasedClassifier.DoubleTableResult... dtr) This method plots an array of AbstractScoreBasedClassifier.DoubleTableResults in one image.

Uses of REnvironment in de.jstacs.classifiers.utils

Methods in de.jstacs.classifiers.utils with parameters of type REnvironment

Modifier and Type	Method and Description
static ImageResult	ClassificationVisualizer.getFancyScatterplot(AbstractScoreBasedClassifier cl1, AbstractScoreBasedClassifier cl2, REnvironment e, DataSet... data) Scatters the classification scores of two binary classifiers for given data.
static ImageResult	ClassificationVisualizer.getScatterplot(AbstractScoreBasedClassifier cl1, AbstractScoreBasedClassifier cl2, DataSet class0, DataSet class1, REnvironment e, boolean drawThreshold) This method returns an ImageResult containing a scatter plot of the scores for the given classifiers cl1 and cl2.
static ImageResult	ClassificationVisualizer.plotScores(AbstractScoreBasedClassifier cl, DataSet class0, DataSet class1, REnvironment e, int bins, double density, String plotOptions) This method returns an ImageResult containing a plot of the histograms of the scores.
static void	ClassificationVisualizer.plotScores(AbstractScoreBasedClassifier cl, DataSet class0, DataSet class1, REnvironment e, int bins, double density, String plotOptions, String fName) This method creates a pdf containing a plot of the histograms of the scores.

Uses of REnvironment in de.jstacs.data

Methods in de.jstacs.data with parameters of type REnvironment

Modifier and Type	Method and Description
static ImageResult	DinucleotideProperty.getPropertyImage(DataSet original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height)
static ImageResult	DinucleotideProperty.getPropertyImage(Sequence original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height)

Uses of REnvironment in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type REnvironment

Modifier and Type	Method and Description
static ImageResult	MotifDiscovererToolBox.plot(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, MotifDiscoverer.KindOfProfile kind) This method creates a simple plot of the profile of scores for a sequence and a start position.
static ImageResult	MotifDiscovererToolBox.plotAndAnnotate(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, double yMin, double yMax, double threshold, MotifDiscoverer.KindOfProfile kind) This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot that have a higher score than threshold.

Uses of REnvironment in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous with parameters of type REnvironment

Modifier and Type	Method and Description
static BufferedImage	TwoPointEvaluater.getImage(DataSet d, double[] weights, REnvironment r, double alpha, int... borders)
static BufferedImage	TwoPointEvaluater.getImage(double[][] mi, REnvironment r) This method can be used to create an image of a mutual information matrix.