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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`.

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.

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