Uses of Class
sc.fiji.snt.analysis.SNTChart

Packages that use SNTChart

Package	Description
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.analysis.sholl.math	Statistical analysis of Sholl data
sc.fiji.snt.plugin	SNT add-ons as IJ2 commands
sc.fiji.snt.viewer	Visualization of reconstructions

Uses of SNTChart in sc.fiji.snt.analysis

Methods in sc.fiji.snt.analysis that return SNTChart

Modifier and Type	Method	Description
static SNTChart	AnalysisUtils.boxPlot(String valueAxisLabel, org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset dataset)
static SNTChart	SNTChart.combine(Collection<SNTChart> charts)	Combines a collection of charts into a multipanel montage.
static SNTChart	SNTChart.combine(Collection<SNTChart> charts, boolean labelPanels)	Combines a collection of charts into a multipanel montage.
static SNTChart	SNTChart.combine(Collection<SNTChart> charts, int rows, int cols, boolean labelPanels)	Combines a collection of charts into a multipanel montage.
static SNTChart	SNTChart.combine(Collection<SNTChart> charts, String commonTitle, int rows, int cols, boolean labelPanels)	Combines a collection of charts into a multipanel montage.
SNTChart	NodeStatistics.getAnnotatedFrequencyHistogram(int depth, String hemisphere, Tree tree)	Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified hemisphere.
SNTChart	NodeStatistics.getAnnotatedHistogram()	Retrieves the histogram of count frequencies across brain areas.
SNTChart	NodeStatistics.getAnnotatedHistogram(int depth)	Retrieves the histogram of count frequencies across brain areas of the specified ontology level.
SNTChart	TreeStatistics.getAnnotatedLengthHistogram()	Retrieves the of cable length frequencies across brain areas.
SNTChart	TreeStatistics.getAnnotatedLengthHistogram(int depth)	Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level.
SNTChart	TreeStatistics.getAnnotatedLengthHistogram(int depth, String hemisphere)	Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level across the specified hemisphere.
protected SNTChart	TreeStatistics.getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map, int depth, String secondaryLabel)
protected SNTChart	TreeStatistics.getAnnotatedLengthsByHemisphereHistogram(int depth)
SNTChart	GroupedTreeStatistics.getBoxPlot(String measurement)	Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).
SNTChart	GroupedTreeStatistics.getBoxPlot(String feature, int depth, double cutoff, boolean normalize)	Assembles a Box and Whisker Plot for the specified feature.
SNTChart	GroupedTreeStatistics.getBoxPlot(String feature, Collection<BrainAnnotation> annotations)	Assembles a Box and Whisker Plot for the specified feature (absolute measurements).
SNTChart	GroupedTreeStatistics.getBoxPlot(String feature, Collection<BrainAnnotation> annotations, double cutoff, boolean normalize)	Assembles a Box and Whisker Plot for the specified feature.
SNTChart	MultiTreeStatistics.getBoxPlot(String measurement)	Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).
SNTChart	RootAngleAnalyzer.getDensityPlot()	Generates a density plot of the root angles using the fitted von Mises distribution.
static SNTChart	RootAngleAnalyzer.getDensityPlot(List<RootAngleAnalyzer> analyzers)
SNTChart	GroupedTreeStatistics.getFlowPlot(String feature, int depth)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth.
SNTChart	GroupedTreeStatistics.getFlowPlot(String feature, int depth, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth
SNTChart	GroupedTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	GroupedTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature.
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, int depth)
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, int depth, double cutoff, boolean normalize)
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations)
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)
SNTChart	TreeStatistics.getFlowPlot(String feature, int depth)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth.
SNTChart	TreeStatistics.getFlowPlot(String feature, int depth, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, no cutoff value, and all of the brain regions of the specified ontology depth
SNTChart	TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature.
SNTChart	GroupedTreeStatistics.getHistogram(String measurement)	Gets the relative frequencies histogram for a univariate measurement.
SNTChart	MultiTreeStatistics.getHistogram(String metric)
SNTChart	NodeStatistics.getHistogram(String metric)	Gets the relative frequencies histogram for a univariate measurement.
SNTChart	RootAngleAnalyzer.getHistogram(boolean polar)	Assembles the histogram distribution of root angles.
static SNTChart	RootAngleAnalyzer.getHistogram(List<RootAngleAnalyzer> analyzers, boolean polar)
static SNTChart	SNTChart.getHistogram(SNTTable table, boolean polar)
static SNTChart	SNTChart.getHistogram(SNTTable table, int[] columnIndices, boolean polar)	Creates a histogram from the given table.
static SNTChart	SNTChart.getHistogram(SNTTable table, Collection<String> columnHeaders, boolean polar)	Creates a histogram from the given table.
SNTChart	TreeStatistics.getHistogram(String metric)	Retrieves the histogram of relative frequencies histogram for a univariate measurement.
protected SNTChart	TreeStatistics.getHistogram(String normMeasurement, sc.fiji.snt.analysis.AnalysisUtils.HistogramDatasetPlus datasetPlus)
SNTChart	GroupedTreeStatistics.getPolarHistogram(String measurement)	Gets the relative frequencies histogram for a univariate measurement as a polar (rose) plot assuming a data range between [0-360].
SNTChart	MultiTreeStatistics.getPolarHistogram(String metric)
SNTChart	TreeStatistics.getPolarHistogram(String metric)	Assembles a polar histogram for the specified metric (assumed to be an angular measurements (e.g., branch angles, path orientations).
static SNTChart	AnalysisUtils.polarPlot(String title, List<double[][]> seriesData, List<Color> seriesColors)	Generates a polar plot
static SNTChart	AnalysisUtils.ringPlot(String title, HashMap<String,Double> data, HashMap<String,Color> colors)	Generates a ring plot (aka donut plot).
static SNTChart	AnalysisUtils.ringPlot(String title, HashMap<GrowthAnalyzer.GrowthPhaseType,Double> phaseFrequencies)	Creates a ring plot of growth phases.

Methods in sc.fiji.snt.analysis that return types with arguments of type SNTChart

Modifier and Type	Method	Description
static List<SNTChart>	SNTChart.openCharts()

Methods in sc.fiji.snt.analysis with parameters of type SNTChart

Modifier and Type	Method	Description
void	SNTChart.applyStyle(SNTChart template)
void	SNTChart.replace(SNTChart other)	Replaces the current chart with the specified instance

Method parameters in sc.fiji.snt.analysis with type arguments of type SNTChart

Modifier and Type	Method	Description
static SNTChart	SNTChart.combine(Collection<SNTChart> charts)	Combines a collection of charts into a multipanel montage.
static SNTChart	SNTChart.combine(Collection<SNTChart> charts, boolean labelPanels)	Combines a collection of charts into a multipanel montage.
static SNTChart	SNTChart.combine(Collection<SNTChart> charts, int rows, int cols, boolean labelPanels)	Combines a collection of charts into a multipanel montage.
static SNTChart	SNTChart.combine(Collection<SNTChart> charts, String commonTitle, int rows, int cols, boolean labelPanels)	Combines a collection of charts into a multipanel montage.
static ij.ImagePlus	SNTChart.combineAsImagePlus(Collection<SNTChart> charts)	Combines a collection of charts into a ImageJ1 stack.
static void	SNTChart.tile(Collection<SNTChart> charts)	Tiles specified charts displaying them on a grid.

Uses of SNTChart in sc.fiji.snt.analysis.sholl.math

Methods in sc.fiji.snt.analysis.sholl.math that return SNTChart

Modifier and Type	Method	Description
SNTChart	PolarProfileStats.getPlot()
SNTChart	PolarProfileStats.getPlot(String colormap)	Returns the polar plot using the specified colormap.
SNTChart	PolarProfileStats.getPlot(net.imglib2.display.ColorTable colorTable)	Returns the polar plot using the specified colormap.

Uses of SNTChart in sc.fiji.snt.plugin

Methods in sc.fiji.snt.plugin that return SNTChart

Modifier and Type	Method	Description
SNTChart	StrahlerCmd.getBoxPlot(String metric)	Returns a boxplot for the specified metric, in which data is grouped by order.
SNTChart	PathOrderAnalysisCmd.getChart()	A variant of PathOrderAnalysisCmd.getCategoryChart() that returns the Analysis chart as a SNTChart object.
SNTChart	StrahlerCmd.getChart()	Returns the 'complete Strahler plot' (e.g., all metrics in a single plot).
SNTChart	StrahlerCmd.getChart(String metric)	Returns a 'Strahler plot' for the specified metric.
SNTChart	StrahlerCmd.getHistogram(String metric)	Returns a histogram for the specified metric, in which data is grouped by order.

Uses of SNTChart in sc.fiji.snt.viewer

Methods in sc.fiji.snt.viewer that return SNTChart

Modifier and Type	Method	Description
SNTChart	Viewer2D.getChart()	Gets the current viewer as a SNTChart object