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| 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. 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 |
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| 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.DoubleTableResults in one
image. |
| Uses of REnvironment in de.jstacs.classifiers.utils |
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| 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 |
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| 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 |
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| 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 |
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| Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous with parameters of type REnvironment | |
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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. |
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