Uses of Class
sc.fiji.snt.analysis.SNTChart
Packages that use SNTChart
Package
Description
Analysis of
Trees.Statistical analysis of Sholl data
SNT add-ons as IJ2 commands
Visualization of reconstructions
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Uses of SNTChart in sc.fiji.snt.analysis
Methods in sc.fiji.snt.analysis that return SNTChartModifier and TypeMethodDescriptionstatic SNTChartAnalysisUtils.boxPlot(String valueAxisLabel, org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset dataset) static SNTChartSNTChart.combine(Collection<SNTChart> charts) Combines a collection of charts into a multipanel montage.static SNTChartSNTChart.combine(Collection<SNTChart> charts, boolean labelPanels) Combines a collection of charts into a multipanel montage.static SNTChartSNTChart.combine(Collection<SNTChart> charts, int rows, int cols, boolean labelPanels) Combines a collection of charts into a multipanel montage.static SNTChartSNTChart.combine(Collection<SNTChart> charts, String commonTitle, int rows, int cols, boolean labelPanels) Combines a collection of charts into a multipanel montage.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.NodeStatistics.getAnnotatedHistogram()Retrieves the histogram of count frequencies across brain areas.NodeStatistics.getAnnotatedHistogram(int depth) Retrieves the histogram of count frequencies across brain areas of the specified ontology level.TreeStatistics.getAnnotatedLengthHistogram()Retrieves the of cable length frequencies across brain areas.TreeStatistics.getAnnotatedLengthHistogram(int depth) Retrieves the histogram of cable length frequencies across brain areas of the specified ontology level.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 SNTChartTreeStatistics.getAnnotatedLengthHistogram(Map<BrainAnnotation, Double> map, int depth, String secondaryLabel) protected SNTChartTreeStatistics.getAnnotatedLengthsByHemisphereHistogram(int depth) GroupedTreeStatistics.getBoxPlot(String measurement) Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).GroupedTreeStatistics.getBoxPlot(String feature, int depth, double cutoff, boolean normalize) Assembles a Box and Whisker Plot for the specified feature.GroupedTreeStatistics.getBoxPlot(String feature, Collection<BrainAnnotation> annotations) Assembles a Box and Whisker Plot for the specified feature (absolute measurements).GroupedTreeStatistics.getBoxPlot(String feature, Collection<BrainAnnotation> annotations, double cutoff, boolean normalize) Assembles a Box and Whisker Plot for the specified feature.MultiTreeStatistics.getBoxPlot(String measurement) Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).RootAngleAnalyzer.getDensityPlot()Generates a density plot of the root angles using the fitted von Mises distribution.static SNTChartRootAngleAnalyzer.getDensityPlot(List<RootAngleAnalyzer> analyzers) 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.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 depthGroupedTreeStatistics.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.GroupedTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize) Assembles a Flow plot (aka Sankey diagram) for the specified feature.MultiTreeStatistics.getFlowPlot(String feature, int depth) MultiTreeStatistics.getFlowPlot(String feature, int depth, double cutoff, boolean normalize) MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations) MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize) MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize) 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.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 depthTreeStatistics.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.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.TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize) Assembles a Flow plot (aka Sankey diagram) for the specified feature.GroupedTreeStatistics.getHistogram(String measurement) Gets the relative frequencies histogram for a univariate measurement.MultiTreeStatistics.getHistogram(String metric) NodeStatistics.getHistogram(String metric) Gets the relative frequencies histogram for a univariate measurement.RootAngleAnalyzer.getHistogram(boolean polar) Assembles the histogram distribution of root angles.static SNTChartRootAngleAnalyzer.getHistogram(List<RootAngleAnalyzer> analyzers, boolean polar) static SNTChartSNTChart.getHistogram(SNTTable table, boolean polar) static SNTChartSNTChart.getHistogram(SNTTable table, int[] columnIndices, boolean polar) Creates a histogram from the given table.static SNTChartSNTChart.getHistogram(SNTTable table, Collection<String> columnHeaders, boolean polar) Creates a histogram from the given table.TreeStatistics.getHistogram(String metric) Retrieves the histogram of relative frequencies histogram for a univariate measurement.protected SNTChartTreeStatistics.getHistogram(String normMeasurement, sc.fiji.snt.analysis.AnalysisUtils.HistogramDatasetPlus datasetPlus) 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].MultiTreeStatistics.getPolarHistogram(String metric) 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 SNTChartGenerates a polar plotstatic SNTChartGenerates a ring plot (aka donut plot).static SNTChartAnalysisUtils.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 SNTChartMethods in sc.fiji.snt.analysis with parameters of type SNTChartModifier and TypeMethodDescriptionvoidSNTChart.applyStyle(SNTChart template) voidReplaces the current chart with the specified instanceMethod parameters in sc.fiji.snt.analysis with type arguments of type SNTChartModifier and TypeMethodDescriptionstatic SNTChartSNTChart.combine(Collection<SNTChart> charts) Combines a collection of charts into a multipanel montage.static SNTChartSNTChart.combine(Collection<SNTChart> charts, boolean labelPanels) Combines a collection of charts into a multipanel montage.static SNTChartSNTChart.combine(Collection<SNTChart> charts, int rows, int cols, boolean labelPanels) Combines a collection of charts into a multipanel montage.static SNTChartSNTChart.combine(Collection<SNTChart> charts, String commonTitle, int rows, int cols, boolean labelPanels) Combines a collection of charts into a multipanel montage.static ij.ImagePlusSNTChart.combineAsImagePlus(Collection<SNTChart> charts) Combines a collection of charts into a ImageJ1 stack.static voidSNTChart.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 -
Uses of SNTChart in sc.fiji.snt.plugin
Methods in sc.fiji.snt.plugin that return SNTChartModifier and TypeMethodDescriptionStrahlerCmd.getBoxPlot(String metric) Returns a boxplot for the specified metric, in which data is grouped by order.PathOrderAnalysisCmd.getChart()A variant ofPathOrderAnalysisCmd.getCategoryChart()that returns the Analysis chart as aSNTChartobject.StrahlerCmd.getChart()Returns the 'complete Strahler plot' (e.g., all metrics in a single plot).Returns a 'Strahler plot' for the specified metric.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