cytoflow package

cytoflow

cytoflow is a package for quantitative, reproducible analysis of flow cytometry data.

Written by Brian Teague, bpteague@gmail.com

Copyright Massachusetts Institute of Technology 2015-2018

Copyright Brian Teague 2018-2025

cytoflow.empty_del(self)

Subpackages

• cytoflow.operations package
  • cytoflow.operations
  • Submodules
    • cytoflow.operations.autofluorescence
    • AutofluorescenceOp
      • AutofluorescenceOp.channels
      • AutofluorescenceOp.blank_file
      • AutofluorescenceOp.blank_file_conditions
      • AutofluorescenceOp.estimate()
      • AutofluorescenceOp.apply()
      • AutofluorescenceOp.default_view()
    • AutofluorescenceDiagnosticView
      • AutofluorescenceDiagnosticView.op
      • AutofluorescenceDiagnosticView.plot()
    • cytoflow.operations.base_op_views
    • OpView
      • OpView.op
    • Op1DView
      • Op1DView.channel
      • Op1DView.scale
    • Op2DView
      • Op2DView.xchannel
      • Op2DView.ychannel
      • Op2DView.xscale
      • Op2DView.yscale
    • ByView
      • ByView.facets
      • ByView.by
      • ByView.enum_plots()
      • ByView.plot()
    • By1DView
    • By2DView
    • NullView
    • AnnotatingView
      • AnnotatingView.plot()
    • cytoflow.operations.bead_calibration
    • BeadCalibrationOp
      • BeadCalibrationOp.units
      • BeadCalibrationOp.beads_file
      • BeadCalibrationOp.beads
      • BeadCalibrationOp.bead_peak_quantile
      • BeadCalibrationOp.bead_brightness_threshold
      • BeadCalibrationOp.bead_brightness_cutoff
      • BeadCalibrationOp.bead_histogram_bins
      • BeadCalibrationOp.force_linear
      • BeadCalibrationOp.estimate()
      • BeadCalibrationOp.apply()
      • BeadCalibrationOp.default_view()
      • BeadCalibrationOp.BEADS
    • BeadCalibrationDiagnostic
      • BeadCalibrationDiagnostic.op
      • BeadCalibrationDiagnostic.plot()
    • cytoflow.operations.binning
    • BinningOp
      • BinningOp.name
      • BinningOp.channel
      • BinningOp.scale
      • BinningOp.bin_width
      • BinningOp.apply()
      • BinningOp.default_view()
    • BinningView
      • BinningView.channel
      • BinningView.scale
      • BinningView.op
      • BinningView.subset
      • BinningView.xfacet
      • BinningView.yfacet
      • BinningView.huefacet
      • BinningView.huescale
      • BinningView.plot()
    • cytoflow.operations.bleedthrough_linear
    • BleedthroughLinearOp
      • BleedthroughLinearOp.controls
      • BleedthroughLinearOp.spillover
      • BleedthroughLinearOp.control_conditions
      • BleedthroughLinearOp.estimate()
      • BleedthroughLinearOp.set_from_fcs()
      • BleedthroughLinearOp.apply()
      • BleedthroughLinearOp.default_view()
    • BleedthroughLinearDiagnostic
      • BleedthroughLinearDiagnostic.op
      • BleedthroughLinearDiagnostic.subset
      • BleedthroughLinearDiagnostic.plot()
    • cytoflow.operations.category
    • CategoryOp
      • CategoryOp.name
      • CategoryOp.subsets
      • CategoryOp.default
      • CategoryOp.apply()
    • cytoflow.operations.centroid
    • cytoflow.operations.channel_stat
    • ChannelStatisticOp
      • ChannelStatisticOp.name
      • ChannelStatisticOp.channel
      • ChannelStatisticOp.function
      • ChannelStatisticOp.by
      • ChannelStatisticOp.subset
      • ChannelStatisticOp.apply()
    • cytoflow.operations.color_translation
    • ColorTranslationOp
      • ColorTranslationOp.controls
      • ColorTranslationOp.mixture_model
      • ColorTranslationOp.linear_model
      • ColorTranslationOp.control_conditions
      • ColorTranslationOp.estimate()
      • ColorTranslationOp.apply()
      • ColorTranslationOp.default_view()
    • ColorTranslationDiagnostic
      • ColorTranslationDiagnostic.name
      • ColorTranslationDiagnostic.op
      • ColorTranslationDiagnostic.subset
      • ColorTranslationDiagnostic.plot()
    • cytoflow.operations.density
    • DensityGateOp
      • DensityGateOp.name
      • DensityGateOp.xchannel
      • DensityGateOp.ychannel
      • DensityGateOp.xscale
      • DensityGateOp.yscale
      • DensityGateOp.keep
      • DensityGateOp.bins
      • DensityGateOp.min_quantile
      • DensityGateOp.max_quantile
      • DensityGateOp.sigma
      • DensityGateOp.by
      • DensityGateOp.estimate()
      • DensityGateOp.apply()
      • DensityGateOp.default_view()
    • DensityGateView
      • DensityGateView.facets
      • DensityGateView.by
      • DensityGateView.xchannel
      • DensityGateView.ychannel
      • DensityGateView.xscale
      • DensityGateView.yscale
      • DensityGateView.op
      • DensityGateView.huefacet
      • DensityGateView.subset
      • DensityGateView.xfacet
      • DensityGateView.yfacet
      • DensityGateView.huescale
      • DensityGateView.plot()
    • cytoflow.operations.flowclean
    • FlowCleanOp
      • FlowCleanOp.name
      • FlowCleanOp.time_channel
      • FlowCleanOp.channels
      • FlowCleanOp.scale
      • FlowCleanOp.segment_size
      • FlowCleanOp.density_cutoff
      • FlowCleanOp.max_discontinuity
      • FlowCleanOp.max_drift
      • FlowCleanOp.max_mean_drift
      • FlowCleanOp.segment_cutoff
      • FlowCleanOp.detect_worst_channels_range
      • FlowCleanOp.detect_worst_channels_sd
      • FlowCleanOp.measures
      • FlowCleanOp.dont_clean
      • FlowCleanOp.force_clean
      • FlowCleanOp.tube_status
      • FlowCleanOp.tube_statistics
      • FlowCleanOp.estimate()
      • FlowCleanOp.apply()
      • FlowCleanOp.default_view()
    • FlowCleanDiagnostic
      • FlowCleanDiagnostic.op
      • FlowCleanDiagnostic.enum_plots()
      • FlowCleanDiagnostic.plot()
    • cytoflow.operations.flowpeaks
    • FlowPeaksOp
      • FlowPeaksOp.name
      • FlowPeaksOp.channels
      • FlowPeaksOp.scale
      • FlowPeaksOp.by
      • FlowPeaksOp.h
      • FlowPeaksOp.h0
      • FlowPeaksOp.tol
      • FlowPeaksOp.merge_dist
      • FlowPeaksOp.find_outliers
      • FlowPeaksOp.Statistics
      • FlowPeaksOp.estimate()
      • FlowPeaksOp.apply()
      • FlowPeaksOp.default_view()
    • FlowPeaks1DView
      • FlowPeaks1DView.facets
      • FlowPeaks1DView.by
      • FlowPeaks1DView.channel
      • FlowPeaks1DView.scale
      • FlowPeaks1DView.op
      • FlowPeaks1DView.subset
      • FlowPeaks1DView.xfacet
      • FlowPeaks1DView.yfacet
      • FlowPeaks1DView.huefacet
      • FlowPeaks1DView.huescale
      • FlowPeaks1DView.plot()
    • FlowPeaks2DView
      • FlowPeaks2DView.facets
      • FlowPeaks2DView.by
      • FlowPeaks2DView.xchannel
      • FlowPeaks2DView.ychannel
      • FlowPeaks2DView.xscale
      • FlowPeaks2DView.yscale
      • FlowPeaks2DView.op
      • FlowPeaks2DView.huechannel
      • FlowPeaks2DView.subset
      • FlowPeaks2DView.xfacet
      • FlowPeaks2DView.yfacet
      • FlowPeaks2DView.huefacet
      • FlowPeaks2DView.huescale
      • FlowPeaks2DView.plot()
    • FlowPeaks2DDensityView
      • FlowPeaks2DDensityView.facets
      • FlowPeaks2DDensityView.by
      • FlowPeaks2DDensityView.xchannel
      • FlowPeaks2DDensityView.ychannel
      • FlowPeaks2DDensityView.xscale
      • FlowPeaks2DDensityView.yscale
      • FlowPeaks2DDensityView.op
      • FlowPeaks2DDensityView.subset
      • FlowPeaks2DDensityView.xfacet
      • FlowPeaks2DDensityView.yfacet
      • FlowPeaks2DDensityView.huefacet
      • FlowPeaks2DDensityView.huescale
      • FlowPeaks2DDensityView.plot()
    • cytoflow.operations.frame_stat
    • FrameStatisticOp
      • FrameStatisticOp.name
      • FrameStatisticOp.function
      • FrameStatisticOp.by
      • FrameStatisticOp.subset
      • FrameStatisticOp.apply()
    • cytoflow.operations.gaussian
    • GaussianMixtureOp
      • GaussianMixtureOp.name
      • GaussianMixtureOp.channels
      • GaussianMixtureOp.scale
      • GaussianMixtureOp.num_components
      • GaussianMixtureOp.sigma
      • GaussianMixtureOp.by
      • GaussianMixtureOp.posteriors
      • GaussianMixtureOp.Statistics
      • GaussianMixtureOp.estimate()
      • GaussianMixtureOp.apply()
      • GaussianMixtureOp.default_view()
    • GaussianMixture1DView
      • GaussianMixture1DView.facets
      • GaussianMixture1DView.by
      • GaussianMixture1DView.channel
      • GaussianMixture1DView.scale
      • GaussianMixture1DView.op
      • GaussianMixture1DView.subset
      • GaussianMixture1DView.xfacet
      • GaussianMixture1DView.yfacet
      • GaussianMixture1DView.huefacet
      • GaussianMixture1DView.huescale
      • GaussianMixture1DView.plot()
    • poly_area()
    • GaussianMixture2DView
      • GaussianMixture2DView.facets
      • GaussianMixture2DView.by
      • GaussianMixture2DView.xchannel
      • GaussianMixture2DView.ychannel
      • GaussianMixture2DView.xscale
      • GaussianMixture2DView.yscale
      • GaussianMixture2DView.op
      • GaussianMixture2DView.huechannel
      • GaussianMixture2DView.subset
      • GaussianMixture2DView.xfacet
      • GaussianMixture2DView.yfacet
      • GaussianMixture2DView.huefacet
      • GaussianMixture2DView.huescale
      • GaussianMixture2DView.plot()
    • cytoflow.operations.hierarchy
    • HierarchyOp
      • HierarchyOp.name
      • HierarchyOp.gates
      • HierarchyOp.default
      • HierarchyOp.apply()
    • cytoflow.operations.i_operation
    • IOperation
      • IOperation.id
      • IOperation.friendly_id
      • IOperation.name
      • IOperation.estimate()
      • IOperation.apply()
      • IOperation.default_view()
    • cytoflow.operations.import_op
    • Tube
      • Tube.file
      • Tube.conditions
      • Tube.conditions_equal()
    • ImportOp
      • ImportOp.conditions
      • ImportOp.tubes
      • ImportOp.channels
      • ImportOp.events
      • ImportOp.name_metadata
      • ImportOp.data_set
      • ImportOp.ignore_v
      • ImportOp.apply()
    • check_tube()
    • autodetect_name_metadata()
    • parse_tube()
    • cytoflow.operations.kmeans
    • KMeansOp
      • KMeansOp.name
      • KMeansOp.channels
      • KMeansOp.scale
      • KMeansOp.num_clusters
      • KMeansOp.by
      • KMeansOp.Statistics
      • KMeansOp.estimate()
      • KMeansOp.apply()
      • KMeansOp.default_view()
    • KMeans1DView
      • KMeans1DView.op
      • KMeans1DView.facets
      • KMeans1DView.by
      • KMeans1DView.channel
      • KMeans1DView.scale
      • KMeans1DView.subset
      • KMeans1DView.xfacet
      • KMeans1DView.yfacet
      • KMeans1DView.huefacet
      • KMeans1DView.huescale
      • KMeans1DView.plot()
    • KMeans2DView
      • KMeans2DView.op
      • KMeans2DView.facets
      • KMeans2DView.by
      • KMeans2DView.xchannel
      • KMeans2DView.ychannel
      • KMeans2DView.xscale
      • KMeans2DView.yscale
      • KMeans2DView.huechannel
      • KMeans2DView.subset
      • KMeans2DView.xfacet
      • KMeans2DView.yfacet
      • KMeans2DView.huefacet
      • KMeans2DView.huescale
      • KMeans2DView.plot()
    • cytoflow.operations.mst
    • ConditionSelectionOp
      • ConditionSelectionOp.name
      • ConditionSelectionOp.condition
      • ConditionSelectionOp.condition_values
      • ConditionSelectionOp.apply()
    • MSTOp
      • MSTOp.name
      • MSTOp.condition
      • MSTOp.condition_values
      • MSTOp.apply()
      • MSTOp.default_view()
    • MSTSelectionView
      • MSTSelectionView.op
      • MSTSelectionView.statistic
      • MSTSelectionView.locations
      • MSTSelectionView.locations_level
      • MSTSelectionView.locations_features
      • MSTSelectionView.variable
      • MSTSelectionView.feature
      • MSTSelectionView.style
      • MSTSelectionView.scale
      • MSTSelectionView.size_function
      • MSTSelectionView.metric
      • MSTSelectionView.subset
      • MSTSelectionView.plot()
    • cytoflow.operations.pca
    • PCAOp
      • PCAOp.name
      • PCAOp.channels
      • PCAOp.scale
      • PCAOp.num_components
      • PCAOp.by
      • PCAOp.whiten
      • PCAOp.Statistics
      • PCAOp.estimate()
      • PCAOp.apply()
    • cytoflow.operations.polygon
    • PolygonOp
      • PolygonOp.name
      • PolygonOp.vertices
      • PolygonOp.apply()
      • PolygonOp.default_view()
    • ScatterplotPolygonSelectionView
      • ScatterplotPolygonSelectionView.interactive
      • ScatterplotPolygonSelectionView.xchannel
      • ScatterplotPolygonSelectionView.ychannel
      • ScatterplotPolygonSelectionView.xscale
      • ScatterplotPolygonSelectionView.yscale
      • ScatterplotPolygonSelectionView.op
      • ScatterplotPolygonSelectionView.huechannel
      • ScatterplotPolygonSelectionView.subset
      • ScatterplotPolygonSelectionView.xfacet
      • ScatterplotPolygonSelectionView.yfacet
      • ScatterplotPolygonSelectionView.huefacet
      • ScatterplotPolygonSelectionView.huescale
      • ScatterplotPolygonSelectionView.plot()
    • DensityPolygonSelectionView
      • DensityPolygonSelectionView.interactive
      • DensityPolygonSelectionView.xchannel
      • DensityPolygonSelectionView.ychannel
      • DensityPolygonSelectionView.xscale
      • DensityPolygonSelectionView.yscale
      • DensityPolygonSelectionView.op
      • DensityPolygonSelectionView.huefacet
      • DensityPolygonSelectionView.subset
      • DensityPolygonSelectionView.xfacet
      • DensityPolygonSelectionView.yfacet
      • DensityPolygonSelectionView.huescale
      • DensityPolygonSelectionView.plot()
    • cytoflow.operations.quad
    • QuadOp
      • QuadOp.name
      • QuadOp.xchannel
      • QuadOp.xthreshold
      • QuadOp.ychannel
      • QuadOp.ythreshold
      • QuadOp.apply()
      • QuadOp.default_view()
    • ScatterplotQuadSelectionView
      • ScatterplotQuadSelectionView.interactive
      • ScatterplotQuadSelectionView.xchannel
      • ScatterplotQuadSelectionView.ychannel
      • ScatterplotQuadSelectionView.xscale
      • ScatterplotQuadSelectionView.yscale
      • ScatterplotQuadSelectionView.op
      • ScatterplotQuadSelectionView.huechannel
      • ScatterplotQuadSelectionView.subset
      • ScatterplotQuadSelectionView.xfacet
      • ScatterplotQuadSelectionView.yfacet
      • ScatterplotQuadSelectionView.huefacet
      • ScatterplotQuadSelectionView.huescale
      • ScatterplotQuadSelectionView.plot()
    • DensityQuadSelectionView
      • DensityQuadSelectionView.interactive
      • DensityQuadSelectionView.xchannel
      • DensityQuadSelectionView.ychannel
      • DensityQuadSelectionView.xscale
      • DensityQuadSelectionView.yscale
      • DensityQuadSelectionView.op
      • DensityQuadSelectionView.huefacet
      • DensityQuadSelectionView.subset
      • DensityQuadSelectionView.xfacet
      • DensityQuadSelectionView.yfacet
      • DensityQuadSelectionView.huescale
      • DensityQuadSelectionView.plot()
    • cytoflow.operations.range
    • RangeOp
      • RangeOp.name
      • RangeOp.channel
      • RangeOp.low
      • RangeOp.high
      • RangeOp.apply()
      • RangeOp.default_view()
    • RangeSelection
      • RangeSelection.interactive
      • RangeSelection.channel
      • RangeSelection.scale
      • RangeSelection.op
      • RangeSelection.subset
      • RangeSelection.xfacet
      • RangeSelection.yfacet
      • RangeSelection.huefacet
      • RangeSelection.huescale
      • RangeSelection.plot()
    • cytoflow.operations.range2d
    • Range2DOp
      • Range2DOp.name
      • Range2DOp.xchannel
      • Range2DOp.xlow
      • Range2DOp.xhigh
      • Range2DOp.ychannel
      • Range2DOp.ylow
      • Range2DOp.yhigh
      • Range2DOp.apply()
      • Range2DOp.default_view()
    • ScatterplotRangeSelection2DView
      • ScatterplotRangeSelection2DView.interactive
      • ScatterplotRangeSelection2DView.xchannel
      • ScatterplotRangeSelection2DView.ychannel
      • ScatterplotRangeSelection2DView.xscale
      • ScatterplotRangeSelection2DView.yscale
      • ScatterplotRangeSelection2DView.op
      • ScatterplotRangeSelection2DView.huechannel
      • ScatterplotRangeSelection2DView.subset
      • ScatterplotRangeSelection2DView.xfacet
      • ScatterplotRangeSelection2DView.yfacet
      • ScatterplotRangeSelection2DView.huefacet
      • ScatterplotRangeSelection2DView.huescale
    • DensityRangeSelection2DView
      • DensityRangeSelection2DView.interactive
      • DensityRangeSelection2DView.xchannel
      • DensityRangeSelection2DView.ychannel
      • DensityRangeSelection2DView.xscale
      • DensityRangeSelection2DView.yscale
      • DensityRangeSelection2DView.op
      • DensityRangeSelection2DView.huefacet
      • DensityRangeSelection2DView.subset
      • DensityRangeSelection2DView.xfacet
      • DensityRangeSelection2DView.yfacet
      • DensityRangeSelection2DView.huescale
    • cytoflow.operations.ratio
    • RatioOp
      • RatioOp.name
      • RatioOp.numerator
      • RatioOp.denominator
      • RatioOp.apply()
    • cytoflow.operations.register
    • RegistrationOp
      • RegistrationOp.channels
      • RegistrationOp.scale
      • RegistrationOp.by
      • RegistrationOp.subset
      • RegistrationOp.kernel
      • RegistrationOp.bw
      • RegistrationOp.gridsize
      • RegistrationOp.estimate()
      • RegistrationOp.apply()
      • RegistrationOp.default_view()
    • RegistrationDiagnosticView
      • RegistrationDiagnosticView.op
      • RegistrationDiagnosticView.enum_plots()
      • RegistrationDiagnosticView.plot()
    • cytoflow.operations.som
    • SOMOp
      • SOMOp.name
      • SOMOp.channels
      • SOMOp.scale
      • SOMOp.consensus_cluster
      • SOMOp.num_iterations
      • SOMOp.by
      • SOMOp.sample
      • SOMOp.width
      • SOMOp.height
      • SOMOp.distance
      • SOMOp.learning_rate
      • SOMOp.sigma
      • SOMOp.min_clusters
      • SOMOp.max_clusters
      • SOMOp.n_resamples
      • SOMOp.resample_frac
      • SOMOp.Statistics
      • SOMOp.estimate()
      • SOMOp.update_consensus_clusters()
      • SOMOp.apply()
      • SOMOp.default_view()
    • SOMDiagnosticView
      • SOMDiagnosticView.op
      • SOMDiagnosticView.plot()
    • cytoflow.operations.threshold
    • ThresholdOp
      • ThresholdOp.name
      • ThresholdOp.channel
      • ThresholdOp.threshold
      • ThresholdOp.apply()
      • ThresholdOp.default_view()
    • ThresholdSelection
      • ThresholdSelection.interactive
      • ThresholdSelection.channel
      • ThresholdSelection.scale
      • ThresholdSelection.op
      • ThresholdSelection.subset
      • ThresholdSelection.xfacet
      • ThresholdSelection.yfacet
      • ThresholdSelection.huefacet
      • ThresholdSelection.huescale
      • ThresholdSelection.plot()
    • cytoflow.operations.tsne
    • tSNEOp
      • tSNEOp.name
      • tSNEOp.channels
      • tSNEOp.scale
      • tSNEOp.by
      • tSNEOp.metric
      • tSNEOp.perplexity
      • tSNEOp.sample
      • tSNEOp.estimate()
      • tSNEOp.apply()
    • cytoflow.operations.xform_stat
    • TransformStatisticOp
      • TransformStatisticOp.name
      • TransformStatisticOp.statistic
      • TransformStatisticOp.feature
      • TransformStatisticOp.function
      • TransformStatisticOp.by
      • TransformStatisticOp.ignore_incomplete_groups
      • TransformStatisticOp.apply()
• cytoflow.scripts package
  • Submodules
    • cytoflow.scripts.channel_voltages
    • main()
    • cytoflow.scripts.fcs_metadata
    • main()
    • cytoflow.scripts.parse_beads
    • main()
    • cytoflow.scripts.split_fcs
    • main()
• cytoflow.utility package
  • cytoflow.utility
  • IterByWrapper
  • Submodules
    • cytoflow.utility.algorithms
    • ci()
    • percentiles()
    • bootstrap()
    • is_inside_sm()
    • polygon_contains()
    • resample()
    • compute_connectivity_matrix()
    • compute_identity_matrix()
    • compute_consensus_matrix()
    • valid_clustering_obj()
    • cluster()
    • ConsensusClustering
      • ConsensusClustering.cluster_range_
      • ConsensusClustering.consensus_k()
      • ConsensusClustering.fit()
      • ConsensusClustering.hist()
      • ConsensusClustering.cdf()
      • ConsensusClustering.area_under_cdf()
      • ConsensusClustering.change_in_area_under_cdf()
      • ConsensusClustering.best_k()
      • ConsensusClustering.plot_auc_cdf()
      • ConsensusClustering.plot_clustermap()
      • ConsensusClustering.plot_hist()
      • ConsensusClustering.plot_cdf()
      • ConsensusClustering.plot_change_area_under_cdf()
    • ConsensusCluster
      • ConsensusCluster.fit()
      • ConsensusCluster.predict()
      • ConsensusCluster.predict_data()
    • cytoflow.utility.custom_traits
    • PositiveInt
      • PositiveInt.info_text
      • PositiveInt.validate()
    • PositiveCInt
      • PositiveCInt.info_text
      • PositiveCInt.validate()
    • PositiveFloat
      • PositiveFloat.info_text
      • PositiveFloat.validate()
    • PositiveCFloat
      • PositiveCFloat.info_text
      • PositiveCFloat.validate()
    • FloatOrNone
      • FloatOrNone.info_text
      • FloatOrNone.validate()
    • CFloatOrNone
      • CFloatOrNone.info_text
      • CFloatOrNone.validate()
    • UnitFloat
      • UnitFloat.validate()
    • IntOrNone
      • IntOrNone.info_text
      • IntOrNone.validate()
    • CIntOrNone
      • CIntOrNone.info_text
      • CIntOrNone.validate()
    • ScaleEnum
      • ScaleEnum.info_text
      • ScaleEnum.get_default_value()
    • Removed
      • Removed.get()
      • Removed.set()
    • Deprecated
      • Deprecated.get()
      • Deprecated.set()
    • ChangedStr
      • ChangedStr.error()
    • cytoflow.utility.cytoflow_errors
    • CytoflowError
    • CytoflowOpError
    • CytoflowViewError
    • CytoflowWarning
    • CytoflowOpWarning
    • CytoflowViewWarning
    • cytoflow.utility.docstring
    • expand_class_attributes()
    • expand_method_parameters()
    • find_section()
    • get_class_attributes()
    • get_method_parameters()
    • cytoflow.utility.fcswrite
    • write_fcs()
    • cytoflow.utility.hlog_scale
    • HlogScale
      • HlogScale.b
      • HlogScale.name
      • HlogScale.inverse()
      • HlogScale.clip()
      • HlogScale.norm()
      • HlogScale.get_mpl_params()
    • MatplotlibHlogScale
      • MatplotlibHlogScale.name
      • MatplotlibHlogScale.get_transform()
      • MatplotlibHlogScale.set_default_locators_and_formatters()
      • MatplotlibHlogScale.HlogTransform
      • MatplotlibHlogScale.InvertedLogicleTransform
    • HlogMajorLocator
      • HlogMajorLocator.set_params()
      • HlogMajorLocator.tick_values()
      • HlogMajorLocator.view_limits()
    • HlogMinorLocator
      • HlogMinorLocator.set_params()
      • HlogMinorLocator.tick_values()
    • hlog_inv()
    • hlog()
    • KneeLocator
      • KneeLocator.transform_y()
      • KneeLocator.find_knee()
      • KneeLocator.plot_knee_normalized()
      • KneeLocator.plot_knee()
      • KneeLocator.elbow
      • KneeLocator.norm_elbow
      • KneeLocator.elbow_y
      • KneeLocator.norm_elbow_y
      • KneeLocator.all_elbows
      • KneeLocator.all_norm_elbows
      • KneeLocator.all_elbows_y
      • KneeLocator.all_norm_elbows_y
    • cytoflow.utility.linear_scale
    • LinearScale
      • LinearScale.name
      • LinearScale.inverse()
      • LinearScale.clip()
      • LinearScale.norm()
      • LinearScale.get_mpl_params()
    • cytoflow.utility.log_scale
    • LogScale
      • LogScale.name
      • LogScale.get_mpl_params()
      • LogScale.inverse()
      • LogScale.clip()
      • LogScale.norm()
    • cytoflow.utility.logging_ext
    • MplFilter
      • MplFilter.filter()
    • cytoflow.utility.logicle_scale
    • LogicleScale
      • LogicleScale.experiment
      • LogicleScale.channel
      • LogicleScale.condition
      • LogicleScale.statistic
      • LogicleScale.W
      • LogicleScale.M
      • LogicleScale.A
      • LogicleScale.r
      • LogicleScale.name
      • LogicleScale.inverse()
      • LogicleScale.clip()
      • LogicleScale.norm()
      • LogicleScale.get_mpl_params()
    • MatplotlibLogicleScale
      • MatplotlibLogicleScale.name
      • MatplotlibLogicleScale.get_transform()
      • MatplotlibLogicleScale.set_default_locators_and_formatters()
      • MatplotlibLogicleScale.LogicleTransform
      • MatplotlibLogicleScale.InvertedLogicleTransform
    • LogicleMajorLocator
      • LogicleMajorLocator.set_params()
      • LogicleMajorLocator.tick_values()
      • LogicleMajorLocator.view_limits()
    • LogicleMinorLocator
      • LogicleMinorLocator.set_params()
      • LogicleMinorLocator.tick_values()
      • LogicleMinorLocator.view_limits()
    • cytoflow.utility.minisom
    • fast_norm()
    • MiniSom
      • MiniSom.Y_HEX_CONV_FACTOR
      • MiniSom.get_weights()
      • MiniSom.get_euclidean_coordinates()
      • MiniSom.convert_map_to_euclidean()
      • MiniSom.activate()
      • MiniSom.winner()
      • MiniSom.update()
      • MiniSom.quantization()
      • MiniSom.random_weights_init()
      • MiniSom.pca_weights_init()
      • MiniSom.train()
      • MiniSom.train_random()
      • MiniSom.train_batch()
      • MiniSom.distance_map()
      • MiniSom.activation_response()
      • MiniSom.quantization_error()
      • MiniSom.quantization_history()
      • MiniSom.distortion_measure()
      • MiniSom.topographic_error()
      • MiniSom.win_map()
      • MiniSom.labels_map()
    • TestMinisom
      • TestMinisom.setUp()
      • TestMinisom.test_inverse_decay_to_zero_function()
      • TestMinisom.test_linear_decay_to_zero_function()
      • TestMinisom.test_inverse_decay_to_one_function()
      • TestMinisom.test_linear_decay_to_one_function()
      • TestMinisom.test_asymptotic_decay_function()
      • TestMinisom.test_fast_norm()
      • TestMinisom.test_euclidean_distance()
      • TestMinisom.test_cosine_distance()
      • TestMinisom.test_manhattan_distance()
      • TestMinisom.test_chebyshev_distance()
      • TestMinisom.test_check_input_len()
      • TestMinisom.test_unavailable_neigh_function()
      • TestMinisom.test_unavailable_distance_function()
      • TestMinisom.test_gaussian()
      • TestMinisom.test_mexican_hat()
      • TestMinisom.test_bubble()
      • TestMinisom.test_triangle()
      • TestMinisom.test_win_map()
      • TestMinisom.test_win_map_indices()
      • TestMinisom.test_labels_map()
      • TestMinisom.test_activation_reponse()
      • TestMinisom.test_activate()
      • TestMinisom.test_distance_from_weights()
      • TestMinisom.test_quantization_error()
      • TestMinisom.test_topographic_error()
      • TestMinisom.test_hexagonal_topographic_error()
      • TestMinisom.test_quantization()
      • TestMinisom.test_distortion_measure()
      • TestMinisom.test_random_seed()
      • TestMinisom.test_train_batch()
      • TestMinisom.test_train_random()
      • TestMinisom.test_train_use_epochs()
      • TestMinisom.test_train_fixed_points()
      • TestMinisom.test_use_epochs_variables()
      • TestMinisom.test_random_weights_init()
      • TestMinisom.test_pca_weights_init()
      • TestMinisom.test_distance_map()
      • TestMinisom.test_pickling()
      • TestMinisom.test_callable_activation_distance()
      • TestMinisom.test_decay_function_value()
      • TestMinisom.test_sigma_decay_function_value()
    • cytoflow.utility.scale
    • IScale
      • IScale.name
      • IScale.experiment
      • IScale.channel
      • IScale.condition
      • IScale.statistic
      • IScale.data
      • IScale.inverse()
      • IScale.clip()
      • IScale.norm()
    • ScaleMixin
    • scale_factory()
    • register_scale()
    • set_default_scale()
    • get_default_scale()
    • cytoflow.utility.util_functions
    • iqr()
    • num_hist_bins()
    • geom_mean()
    • geom_sd()
    • geom_sd_range()
    • geom_sem()
    • geom_sem_range()
    • cartesian()
    • sanitize_identifier()
    • random_string()
    • is_numeric()
    • cov2corr()
• cytoflow.views package
  • cytoflow.views
  • Submodules
    • cytoflow.views.bar_chart
    • BarChartView
      • BarChartView.variable
      • BarChartView.feature
      • BarChartView.error_low
      • BarChartView.error_high
      • BarChartView.scale
      • BarChartView.statistic
      • BarChartView.xfacet
      • BarChartView.yfacet
      • BarChartView.huefacet
      • BarChartView.subset
      • BarChartView.huescale
      • BarChartView.enum_plots()
      • BarChartView.plot()
    • cytoflow.views.base_views
    • BaseView
      • BaseView.xfacet
      • BaseView.yfacet
      • BaseView.huefacet
      • BaseView.huescale
      • BaseView.plot()
    • BaseDataView
      • BaseDataView.subset
      • BaseDataView.plot()
    • Base1DView
      • Base1DView.channel
      • Base1DView.scale
      • Base1DView.plot()
    • Base2DView
      • Base2DView.xchannel
      • Base2DView.ychannel
      • Base2DView.xscale
      • Base2DView.yscale
      • Base2DView.plot()
    • BaseNDView
      • BaseNDView.channels
      • BaseNDView.scale
      • BaseNDView.plot()
    • BaseStatisticsView
      • BaseStatisticsView.statistic
      • BaseStatisticsView.xfacet
      • BaseStatisticsView.yfacet
      • BaseStatisticsView.huefacet
      • BaseStatisticsView.subset
      • BaseStatisticsView.enum_plots()
      • BaseStatisticsView.plot()
    • Base1DStatisticsView
      • Base1DStatisticsView.variable
      • Base1DStatisticsView.feature
      • Base1DStatisticsView.error_low
      • Base1DStatisticsView.error_high
      • Base1DStatisticsView.scale
      • Base1DStatisticsView.plot()
    • Base2DStatisticsView
      • Base2DStatisticsView.variable
      • Base2DStatisticsView.xfeature
      • Base2DStatisticsView.xerror_low
      • Base2DStatisticsView.xerror_high
      • Base2DStatisticsView.yfeature
      • Base2DStatisticsView.yerror_low
      • Base2DStatisticsView.yerror_high
      • Base2DStatisticsView.xscale
      • Base2DStatisticsView.yscale
      • Base2DStatisticsView.plot()
    • cytoflow.views.densityplot
    • DensityView
      • DensityView.huefacet
      • DensityView.xchannel
      • DensityView.ychannel
      • DensityView.xscale
      • DensityView.yscale
      • DensityView.subset
      • DensityView.xfacet
      • DensityView.yfacet
      • DensityView.huescale
      • DensityView.plot()
    • cytoflow.views.export_fcs
    • ExportFCS
      • ExportFCS.base
      • ExportFCS.path
      • ExportFCS.by
      • ExportFCS.keywords
      • ExportFCS.subset
      • ExportFCS.enum_files()
      • ExportFCS.export()
    • cytoflow.views.histogram
    • HistogramView
      • HistogramView.channel
      • HistogramView.scale
      • HistogramView.subset
      • HistogramView.xfacet
      • HistogramView.yfacet
      • HistogramView.huefacet
      • HistogramView.huescale
      • HistogramView.plot()
    • cytoflow.views.histogram_2d
    • Histogram2DView
      • Histogram2DView.xchannel
      • Histogram2DView.ychannel
      • Histogram2DView.xscale
      • Histogram2DView.yscale
      • Histogram2DView.subset
      • Histogram2DView.xfacet
      • Histogram2DView.yfacet
      • Histogram2DView.huefacet
      • Histogram2DView.huescale
      • Histogram2DView.id
      • Histogram2DView.friend_id
      • Histogram2DView.plot()
    • AlphaColormap
    • cytoflow.views.i_selectionview
    • ISelectionView
      • ISelectionView.interactive
    • cytoflow.views.i_view
    • IView
      • IView.id
      • IView.friendly_id
      • IView.plot()
    • cytoflow.views.kde_1d
    • Kde1DView
      • Kde1DView.channel
      • Kde1DView.scale
      • Kde1DView.subset
      • Kde1DView.xfacet
      • Kde1DView.yfacet
      • Kde1DView.huefacet
      • Kde1DView.huescale
      • Kde1DView.plot()
    • cytoflow.views.kde_2d
    • Kde2DView
      • Kde2DView.xchannel
      • Kde2DView.ychannel
      • Kde2DView.xscale
      • Kde2DView.yscale
      • Kde2DView.subset
      • Kde2DView.xfacet
      • Kde2DView.yfacet
      • Kde2DView.huefacet
      • Kde2DView.huescale
      • Kde2DView.plot()
    • cytoflow.views.long_table
    • LongTableView
      • LongTableView.statistic
      • LongTableView.subset
      • LongTableView.plot()
      • LongTableView.export()
    • cytoflow.views.matrix
    • MatrixView
      • MatrixView.statistic
      • MatrixView.xfacet
      • MatrixView.yfacet
      • MatrixView.variable
      • MatrixView.feature
      • MatrixView.style
      • MatrixView.scale
      • MatrixView.size_function
      • MatrixView.subset
      • MatrixView.plot()
      • MatrixView.enum_plots()
    • cytoflow.views.mst
    • MSTView
      • MSTView.statistic
      • MSTView.locations
      • MSTView.locations_level
      • MSTView.locations_features
      • MSTView.variable
      • MSTView.feature
      • MSTView.style
      • MSTView.scale
      • MSTView.size_function
      • MSTView.metric
      • MSTView.subset
      • MSTView.plot()
      • MSTView.enum_plots()
    • cytoflow.views.parallel_coords
    • ParallelCoordinatesView
      • ParallelCoordinatesView.channels
      • ParallelCoordinatesView.scale
      • ParallelCoordinatesView.subset
      • ParallelCoordinatesView.xfacet
      • ParallelCoordinatesView.yfacet
      • ParallelCoordinatesView.huefacet
      • ParallelCoordinatesView.huescale
      • ParallelCoordinatesView.plot()
    • cytoflow.views.radviz
    • RadvizView
      • RadvizView.channels
      • RadvizView.scale
      • RadvizView.subset
      • RadvizView.xfacet
      • RadvizView.yfacet
      • RadvizView.huefacet
      • RadvizView.huescale
      • RadvizView.plot()
    • cytoflow.views.scatterplot
    • ScatterplotView
      • ScatterplotView.huechannel
      • ScatterplotView.xchannel
      • ScatterplotView.ychannel
      • ScatterplotView.xscale
      • ScatterplotView.yscale
      • ScatterplotView.subset
      • ScatterplotView.xfacet
      • ScatterplotView.yfacet
      • ScatterplotView.huefacet
      • ScatterplotView.huescale
      • ScatterplotView.plot()
    • cytoflow.views.stats_1d
    • Stats1DView
      • Stats1DView.variable_scale
      • Stats1DView.variable
      • Stats1DView.feature
      • Stats1DView.error_low
      • Stats1DView.error_high
      • Stats1DView.scale
      • Stats1DView.statistic
      • Stats1DView.xfacet
      • Stats1DView.yfacet
      • Stats1DView.huefacet
      • Stats1DView.subset
      • Stats1DView.huescale
      • Stats1DView.plot()
    • cytoflow.views.stats_2d
    • Stats2DView
      • Stats2DView.variable
      • Stats2DView.xfeature
      • Stats2DView.xerror_low
      • Stats2DView.xerror_high
      • Stats2DView.yfeature
      • Stats2DView.yerror_low
      • Stats2DView.yerror_high
      • Stats2DView.xscale
      • Stats2DView.yscale
      • Stats2DView.statistic
      • Stats2DView.xfacet
      • Stats2DView.yfacet
      • Stats2DView.huefacet
      • Stats2DView.subset
      • Stats2DView.huescale
      • Stats2DView.plot()
    • cytoflow.views.table
    • TableView
      • TableView.statistic
      • TableView.row_facet
      • TableView.column_facet
      • TableView.subrow_facet
      • TableView.subcolumn_facet
      • TableView.fill
      • TableView.subset
      • TableView.plot()
      • TableView.export()
    • cytoflow.views.violin
    • ViolinPlotView
      • ViolinPlotView.variable
      • ViolinPlotView.channel
      • ViolinPlotView.scale
      • ViolinPlotView.subset
      • ViolinPlotView.xfacet
      • ViolinPlotView.yfacet
      • ViolinPlotView.huefacet
      • ViolinPlotView.huescale
      • ViolinPlotView.plot()

Submodules

• cytoflow.experiment
• Experiment
  • Experiment.data
  • Experiment.metadata
  • Experiment.history
  • Experiment.statistics
  • Experiment.channels
  • Experiment.conditions
  • Experiment.subset()
  • Experiment.query()
  • Experiment.clone()
  • Experiment.add_condition()
  • Experiment.add_channel()
  • Experiment.add_events()
  • Experiment.add_events_multi()