Uses of Class de.jstacs.utils.REnvironment

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Uses of Class
de.jstacs.utils.REnvironment

Packages that use REnvironment
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.
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
`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.DoubleTableResult`s in one image.

Uses of REnvironment in de.jstacs.classifiers.utils

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

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

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
`static BufferedImage`	`TwoPointEvaluater.getImage(double[][] mi, REnvironment r)` This method can be used to create an image of a mutual information matrix.