Cytoflow
1.1
Cytoflow program manual
Installation notes
Project Structure
Design decisions & justifications
Writing new
cytoflow
modules
Spinning a new release
cytoflow package
Cytoflow
Docs
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Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
A
A (cytoflow.utility.logicle_scale.LogicleScale attribute)
add_channel() (cytoflow.experiment.Experiment method)
add_condition() (cytoflow.experiment.Experiment method)
add_events() (cytoflow.experiment.Experiment method)
AlphaColormap (class in cytoflow.views.histogram_2d)
AnnotatingView (class in cytoflow.operations.base_op_views)
apply() (cytoflow.operations.autofluorescence.AutofluorescenceOp method)
(cytoflow.operations.bead_calibration.BeadCalibrationOp method)
(cytoflow.operations.binning.BinningOp method)
(cytoflow.operations.bleedthrough_linear.BleedthroughLinearOp method)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp method)
(cytoflow.operations.channel_stat.ChannelStatisticOp method)
(cytoflow.operations.color_translation.ColorTranslationOp method)
(cytoflow.operations.density.DensityGateOp method)
(cytoflow.operations.flowpeaks.FlowPeaksOp method)
(cytoflow.operations.frame_stat.FrameStatisticOp method)
(cytoflow.operations.gaussian.GaussianMixtureOp method)
(cytoflow.operations.i_operation.IOperation method)
(cytoflow.operations.import_op.ImportOp method)
(cytoflow.operations.kmeans.KMeansOp method)
(cytoflow.operations.pca.PCAOp method)
(cytoflow.operations.polygon.PolygonOp method)
(cytoflow.operations.quad.QuadOp method)
(cytoflow.operations.range.RangeOp method)
(cytoflow.operations.range2d.Range2DOp method)
(cytoflow.operations.ratio.RatioOp method)
(cytoflow.operations.threshold.ThresholdOp method)
(cytoflow.operations.xform_stat.TransformStatisticOp method)
autodetect_name_metadata() (in module cytoflow.operations.import_op)
AutofluorescenceDiagnosticView (class in cytoflow.operations.autofluorescence)
AutofluorescenceOp (class in cytoflow.operations.autofluorescence)
B
b (cytoflow.utility.hlog_scale.HlogScale attribute)
BarChartView (class in cytoflow.views.bar_chart)
base (cytoflow.views.export_fcs.ExportFCS attribute)
Base1DStatisticsView (class in cytoflow.views.base_views)
Base1DView (class in cytoflow.views.base_views)
Base2DStatisticsView (class in cytoflow.views.base_views)
Base2DView (class in cytoflow.views.base_views)
BaseDataView (class in cytoflow.views.base_views)
BaseNDView (class in cytoflow.views.base_views)
BaseStatisticsView (class in cytoflow.views.base_views)
BaseView (class in cytoflow.views.base_views)
bead_brightness_cutoff (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
bead_brightness_threshold (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
bead_histogram_bins (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
bead_peak_quantile (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
BeadCalibrationDiagnostic (class in cytoflow.operations.bead_calibration)
BeadCalibrationOp (class in cytoflow.operations.bead_calibration)
BEADS (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
beads (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
beads_file (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
bin_width (cytoflow.operations.binning.BinningOp attribute)
BinningOp (class in cytoflow.operations.binning)
BinningView (class in cytoflow.operations.binning)
bins (cytoflow.operations.density.DensityGateOp attribute)
blank_file (cytoflow.operations.autofluorescence.AutofluorescenceOp attribute)
blank_file_conditions (cytoflow.operations.autofluorescence.AutofluorescenceOp attribute)
BleedthroughLinearDiagnostic (class in cytoflow.operations.bleedthrough_linear)
BleedthroughLinearOp (class in cytoflow.operations.bleedthrough_linear)
BleedthroughPiecewiseDiagnostic (class in cytoflow.operations.bleedthrough_piecewise)
BleedthroughPiecewiseOp (class in cytoflow.operations.bleedthrough_piecewise)
bootstrap() (in module cytoflow.utility.algorithms)
by (cytoflow.operations.base_op_views.ByView attribute)
(cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.density.DensityGateOp attribute)
(cytoflow.operations.density.DensityGateView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DDensityView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
(cytoflow.operations.frame_stat.FrameStatisticOp attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.gaussian.GaussianMixture2DView attribute)
(cytoflow.operations.gaussian.GaussianMixtureOp attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.kmeans.KMeans2DView attribute)
(cytoflow.operations.kmeans.KMeansOp attribute)
(cytoflow.operations.pca.PCAOp attribute)
(cytoflow.operations.xform_stat.TransformStatisticOp attribute)
(cytoflow.views.export_fcs.ExportFCS attribute)
By1DView (class in cytoflow.operations.base_op_views)
By2DView (class in cytoflow.operations.base_op_views)
ByView (class in cytoflow.operations.base_op_views)
C
cartesian() (in module cytoflow.utility.util_functions)
CFloatOrNone (class in cytoflow.utility.custom_traits)
channel (cytoflow.operations.base_op_views.Op1DView attribute)
(cytoflow.operations.binning.BinningOp attribute)
(cytoflow.operations.binning.BinningView attribute)
(cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.range.RangeOp attribute)
(cytoflow.operations.range.RangeSelection attribute)
(cytoflow.operations.threshold.ThresholdOp attribute)
(cytoflow.operations.threshold.ThresholdSelection attribute)
(cytoflow.utility.logicle_scale.LogicleScale attribute)
(cytoflow.utility.scale.IScale attribute)
(cytoflow.views.base_views.Base1DView attribute)
(cytoflow.views.histogram.HistogramView attribute)
(cytoflow.views.kde_1d.Kde1DView attribute)
(cytoflow.views.violin.ViolinPlotView attribute)
channels (cytoflow.experiment.Experiment attribute)
(cytoflow.operations.autofluorescence.AutofluorescenceOp attribute)
(cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
(cytoflow.operations.gaussian.GaussianMixtureOp attribute)
(cytoflow.operations.import_op.ImportOp attribute)
(cytoflow.operations.kmeans.KMeansOp attribute)
(cytoflow.operations.pca.PCAOp attribute)
(cytoflow.views.base_views.BaseNDView attribute)
(cytoflow.views.parallel_coords.ParallelCoordinatesView attribute)
(cytoflow.views.radviz.RadvizView attribute)
ChannelStatisticOp (class in cytoflow.operations.channel_stat)
check_tube() (in module cytoflow.operations.import_op)
ci() (in module cytoflow.utility.algorithms)
CIntOrNone (class in cytoflow.utility.custom_traits)
clear() (cytoflow.utility.matplotlib_widgets.Cursor method)
clip() (cytoflow.utility.hlog_scale.HlogScale method)
(cytoflow.utility.linear_scale.LinearScale method)
(cytoflow.utility.log_scale.LogScale method)
(cytoflow.utility.logicle_scale.LogicleScale method)
(cytoflow.utility.scale.IScale method)
clone() (cytoflow.experiment.Experiment method)
ColorTranslationDiagnostic (class in cytoflow.operations.color_translation)
ColorTranslationOp (class in cytoflow.operations.color_translation)
condition (cytoflow.utility.logicle_scale.LogicleScale attribute)
(cytoflow.utility.scale.IScale attribute)
conditions (cytoflow.experiment.Experiment attribute)
(cytoflow.operations.import_op.ImportOp attribute)
(cytoflow.operations.import_op.Tube attribute)
conditions_equal() (cytoflow.operations.import_op.Tube method)
control_conditions (cytoflow.operations.bleedthrough_linear.BleedthroughLinearOp attribute)
(cytoflow.operations.color_translation.ColorTranslationOp attribute)
controls (cytoflow.operations.bleedthrough_linear.BleedthroughLinearOp attribute)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp attribute)
(cytoflow.operations.color_translation.ColorTranslationOp attribute)
cov2corr() (in module cytoflow.utility.util_functions)
Cursor (class in cytoflow.utility.matplotlib_widgets)
cytoflow (module)
cytoflow.experiment (module)
cytoflow.operations (module)
cytoflow.operations.autofluorescence (module)
cytoflow.operations.base_op_views (module)
cytoflow.operations.bead_calibration (module)
cytoflow.operations.binning (module)
cytoflow.operations.bleedthrough_linear (module)
cytoflow.operations.bleedthrough_piecewise (module)
cytoflow.operations.channel_stat (module)
cytoflow.operations.color_translation (module)
cytoflow.operations.density (module)
cytoflow.operations.flowpeaks (module)
cytoflow.operations.frame_stat (module)
cytoflow.operations.gaussian (module)
cytoflow.operations.i_operation (module)
cytoflow.operations.import_op (module)
cytoflow.operations.kmeans (module)
cytoflow.operations.pca (module)
cytoflow.operations.polygon (module)
cytoflow.operations.quad (module)
cytoflow.operations.range (module)
cytoflow.operations.range2d (module)
cytoflow.operations.ratio (module)
cytoflow.operations.threshold (module)
cytoflow.operations.xform_stat (module)
cytoflow.scripts (module)
cytoflow.scripts.channel_voltages (module)
cytoflow.scripts.fcs_metadata (module)
cytoflow.utility (module)
cytoflow.utility.algorithms (module)
cytoflow.utility.custom_traits (module)
cytoflow.utility.cytoflow_errors (module)
cytoflow.utility.docstring (module)
cytoflow.utility.fcswrite (module)
cytoflow.utility.hlog_scale (module)
cytoflow.utility.linear_scale (module)
cytoflow.utility.log_scale (module)
cytoflow.utility.logicle_scale (module)
cytoflow.utility.matplotlib_widgets (module)
cytoflow.utility.scale (module)
cytoflow.utility.util_functions (module)
cytoflow.views (module)
cytoflow.views.bar_chart (module)
cytoflow.views.base_views (module)
cytoflow.views.densityplot (module)
cytoflow.views.export_fcs (module)
cytoflow.views.histogram (module)
cytoflow.views.histogram_2d (module)
cytoflow.views.i_selectionview (module)
cytoflow.views.i_view (module)
cytoflow.views.kde_1d (module)
cytoflow.views.kde_2d (module)
cytoflow.views.parallel_coords (module)
cytoflow.views.radviz (module)
cytoflow.views.scatterplot (module)
cytoflow.views.stats_1d (module)
cytoflow.views.stats_2d (module)
cytoflow.views.table (module)
cytoflow.views.violin (module)
CytoflowError
CytoflowOpError
CytoflowOpWarning
CytoflowViewError
CytoflowViewWarning
CytoflowWarning
D
data (cytoflow.experiment.Experiment attribute)
(cytoflow.utility.scale.IScale attribute)
data_set (cytoflow.operations.import_op.ImportOp attribute)
default_view() (cytoflow.operations.autofluorescence.AutofluorescenceOp method)
(cytoflow.operations.bead_calibration.BeadCalibrationOp method)
(cytoflow.operations.binning.BinningOp method)
(cytoflow.operations.bleedthrough_linear.BleedthroughLinearOp method)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp method)
(cytoflow.operations.color_translation.ColorTranslationOp method)
(cytoflow.operations.density.DensityGateOp method)
(cytoflow.operations.flowpeaks.FlowPeaksOp method)
(cytoflow.operations.gaussian.GaussianMixtureOp method)
(cytoflow.operations.i_operation.IOperation method)
(cytoflow.operations.kmeans.KMeansOp method)
(cytoflow.operations.polygon.PolygonOp method)
(cytoflow.operations.quad.QuadOp method)
(cytoflow.operations.range.RangeOp method)
(cytoflow.operations.range2d.Range2DOp method)
(cytoflow.operations.threshold.ThresholdOp method)
denominator (cytoflow.operations.ratio.RatioOp attribute)
DensityGateOp (class in cytoflow.operations.density)
DensityGateView (class in cytoflow.operations.density)
DensityView (class in cytoflow.views.densityplot)
Deprecated (class in cytoflow.utility.custom_traits)
E
enum_files() (cytoflow.views.export_fcs.ExportFCS method)
enum_plots() (cytoflow.operations.base_op_views.ByView method)
(cytoflow.views.bar_chart.BarChartView method)
(cytoflow.views.base_views.Base1DStatisticsView method)
(cytoflow.views.base_views.Base2DStatisticsView method)
(cytoflow.views.base_views.BaseStatisticsView method)
(cytoflow.views.stats_1d.Stats1DView method)
(cytoflow.views.stats_2d.Stats2DView method)
error_statistic (cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.Base1DStatisticsView attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
estimate() (cytoflow.operations.autofluorescence.AutofluorescenceOp method)
(cytoflow.operations.bead_calibration.BeadCalibrationOp method)
(cytoflow.operations.bleedthrough_linear.BleedthroughLinearOp method)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp method)
(cytoflow.operations.color_translation.ColorTranslationOp method)
(cytoflow.operations.density.DensityGateOp method)
(cytoflow.operations.flowpeaks.FlowPeaksOp method)
(cytoflow.operations.gaussian.GaussianMixtureOp method)
(cytoflow.operations.i_operation.IOperation method)
(cytoflow.operations.kmeans.KMeansOp method)
(cytoflow.operations.pca.PCAOp method)
events (cytoflow.operations.import_op.ImportOp attribute)
expand_class_attributes() (in module cytoflow.utility.docstring)
expand_method_parameters() (in module cytoflow.utility.docstring)
Experiment (class in cytoflow.experiment)
experiment (cytoflow.utility.logicle_scale.LogicleScale attribute)
(cytoflow.utility.scale.IScale attribute)
export() (cytoflow.views.export_fcs.ExportFCS method)
(cytoflow.views.table.TableView method)
ExportFCS (class in cytoflow.views.export_fcs)
F
facets (cytoflow.operations.base_op_views.ByView attribute)
(cytoflow.operations.density.DensityGateView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DDensityView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DView attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.gaussian.GaussianMixture2DView attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.kmeans.KMeans2DView attribute)
file (cytoflow.operations.import_op.Tube attribute)
fill (cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.frame_stat.FrameStatisticOp attribute)
(cytoflow.operations.xform_stat.TransformStatisticOp attribute)
filter() (cytoflow.MplFilter method)
find_outliers (cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
find_section() (in module cytoflow.utility.docstring)
FloatOrNone (class in cytoflow.utility.custom_traits)
FlowPeaks1DView (class in cytoflow.operations.flowpeaks)
FlowPeaks2DDensityView (class in cytoflow.operations.flowpeaks)
FlowPeaks2DView (class in cytoflow.operations.flowpeaks)
FlowPeaksOp (class in cytoflow.operations.flowpeaks)
force_linear (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
FrameStatisticOp (class in cytoflow.operations.frame_stat)
friend_id (cytoflow.views.histogram_2d.Histogram2DView attribute)
friendly_id (cytoflow.operations.i_operation.IOperation attribute)
(cytoflow.views.i_view.IView attribute)
function (cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.frame_stat.FrameStatisticOp attribute)
(cytoflow.operations.xform_stat.TransformStatisticOp attribute)
G
GaussianMixture1DView (class in cytoflow.operations.gaussian)
GaussianMixture2DView (class in cytoflow.operations.gaussian)
GaussianMixtureOp (class in cytoflow.operations.gaussian)
geom_mean() (in module cytoflow.utility.util_functions)
geom_sd() (in module cytoflow.utility.util_functions)
geom_sd_range() (in module cytoflow.utility.util_functions)
geom_sem() (in module cytoflow.utility.util_functions)
geom_sem_range() (in module cytoflow.utility.util_functions)
get() (cytoflow.utility.custom_traits.Deprecated method)
(cytoflow.utility.custom_traits.Removed method)
get_class_attributes() (in module cytoflow.utility.docstring)
get_default_scale() (in module cytoflow.utility.scale)
get_default_value() (cytoflow.utility.custom_traits.ScaleEnum method)
get_method_parameters() (in module cytoflow.utility.docstring)
get_mpl_params() (cytoflow.utility.hlog_scale.HlogScale method)
(cytoflow.utility.linear_scale.LinearScale method)
(cytoflow.utility.log_scale.LogScale method)
(cytoflow.utility.logicle_scale.LogicleScale method)
get_transform() (cytoflow.utility.hlog_scale.MatplotlibHlogScale method)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale method)
H
h (cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
h0 (cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
has_inverse (cytoflow.utility.hlog_scale.MatplotlibHlogScale.HlogTransform attribute)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.LogicleTransform attribute)
high (cytoflow.operations.range.RangeOp attribute)
Histogram2DView (class in cytoflow.views.histogram_2d)
HistogramView (class in cytoflow.views.histogram)
history (cytoflow.experiment.Experiment attribute)
hlog() (in module cytoflow.utility.hlog_scale)
hlog_inv() (in module cytoflow.utility.hlog_scale)
HlogMajorLocator (class in cytoflow.utility.hlog_scale)
HlogMinorLocator (class in cytoflow.utility.hlog_scale)
HlogScale (class in cytoflow.utility.hlog_scale)
huefacet (cytoflow.operations.binning.BinningView attribute)
(cytoflow.operations.density.DensityGateView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DDensityView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DView attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.gaussian.GaussianMixture2DView attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.kmeans.KMeans2DView attribute)
(cytoflow.operations.polygon.PolygonSelection attribute)
(cytoflow.operations.quad.QuadSelection attribute)
(cytoflow.operations.range.RangeSelection attribute)
(cytoflow.operations.range2d.RangeSelection2D attribute)
(cytoflow.operations.threshold.ThresholdSelection attribute)
(cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.BaseView attribute)
(cytoflow.views.densityplot.DensityView attribute)
(cytoflow.views.histogram.HistogramView attribute)
(cytoflow.views.histogram_2d.Histogram2DView attribute)
(cytoflow.views.kde_1d.Kde1DView attribute)
(cytoflow.views.kde_2d.Kde2DView attribute)
(cytoflow.views.parallel_coords.ParallelCoordinatesView attribute)
(cytoflow.views.radviz.RadvizView attribute)
(cytoflow.views.scatterplot.ScatterplotView attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
(cytoflow.views.stats_2d.Stats2DView attribute)
(cytoflow.views.violin.ViolinPlotView attribute)
huescale (cytoflow.operations.binning.BinningView attribute)
(cytoflow.operations.density.DensityGateView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DDensityView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DView attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.gaussian.GaussianMixture2DView attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.kmeans.KMeans2DView attribute)
(cytoflow.operations.polygon.PolygonSelection attribute)
(cytoflow.operations.quad.QuadSelection attribute)
(cytoflow.operations.range.RangeSelection attribute)
(cytoflow.operations.range2d.RangeSelection2D attribute)
(cytoflow.operations.threshold.ThresholdSelection attribute)
(cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.BaseView attribute)
(cytoflow.views.densityplot.DensityView attribute)
(cytoflow.views.histogram.HistogramView attribute)
(cytoflow.views.histogram_2d.Histogram2DView attribute)
(cytoflow.views.kde_1d.Kde1DView attribute)
(cytoflow.views.kde_2d.Kde2DView attribute)
(cytoflow.views.parallel_coords.ParallelCoordinatesView attribute)
(cytoflow.views.radviz.RadvizView attribute)
(cytoflow.views.scatterplot.ScatterplotView attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
(cytoflow.views.stats_2d.Stats2DView attribute)
(cytoflow.views.violin.ViolinPlotView attribute)
I
id (cytoflow.operations.i_operation.IOperation attribute)
(cytoflow.views.histogram_2d.Histogram2DView attribute)
(cytoflow.views.i_view.IView attribute)
ignore() (cytoflow.utility.matplotlib_widgets.SpanSelector method)
ignore_deprecated (cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp attribute)
ignore_v (cytoflow.operations.import_op.ImportOp attribute)
ImportOp (class in cytoflow.operations.import_op)
info_text (cytoflow.utility.custom_traits.CFloatOrNone attribute)
(cytoflow.utility.custom_traits.CIntOrNone attribute)
(cytoflow.utility.custom_traits.FloatOrNone attribute)
(cytoflow.utility.custom_traits.IntOrNone attribute)
(cytoflow.utility.custom_traits.PositiveCFloat attribute)
(cytoflow.utility.custom_traits.PositiveCInt attribute)
(cytoflow.utility.custom_traits.PositiveFloat attribute)
(cytoflow.utility.custom_traits.PositiveInt attribute)
(cytoflow.utility.custom_traits.ScaleEnum attribute)
input_dims (cytoflow.utility.hlog_scale.MatplotlibHlogScale.HlogTransform attribute)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.LogicleTransform attribute)
interactive (cytoflow.operations.polygon.PolygonSelection attribute)
(cytoflow.operations.quad.QuadSelection attribute)
(cytoflow.operations.range.RangeSelection attribute)
(cytoflow.operations.range2d.RangeSelection2D attribute)
(cytoflow.operations.threshold.ThresholdSelection attribute)
(cytoflow.views.i_selectionview.ISelectionView attribute)
IntOrNone (class in cytoflow.utility.custom_traits)
inverse() (cytoflow.utility.hlog_scale.HlogScale method)
(cytoflow.utility.linear_scale.LinearScale method)
(cytoflow.utility.log_scale.LogScale method)
(cytoflow.utility.logicle_scale.LogicleScale method)
(cytoflow.utility.scale.IScale method)
inverted() (cytoflow.utility.hlog_scale.MatplotlibHlogScale.HlogTransform method)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale.InvertedLogicleTransform method)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.InvertedLogicleTransform method)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.LogicleTransform method)
IOperation (class in cytoflow.operations.i_operation)
iqr() (in module cytoflow.utility.util_functions)
is_numeric() (in module cytoflow.utility.util_functions)
is_separable (cytoflow.utility.hlog_scale.MatplotlibHlogScale.HlogTransform attribute)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.LogicleTransform attribute)
IScale (class in cytoflow.utility.scale)
ISelectionView (class in cytoflow.views.i_selectionview)
IView (class in cytoflow.views.i_view)
K
Kde1DView (class in cytoflow.views.kde_1d)
Kde2DView (class in cytoflow.views.kde_2d)
keep (cytoflow.operations.density.DensityGateOp attribute)
keywords (cytoflow.views.export_fcs.ExportFCS attribute)
KMeans1DView (class in cytoflow.operations.kmeans)
KMeans2DView (class in cytoflow.operations.kmeans)
KMeansOp (class in cytoflow.operations.kmeans)
L
linear_model (cytoflow.operations.color_translation.ColorTranslationOp attribute)
LinearScale (class in cytoflow.utility.linear_scale)
LogicleMajorLocator (class in cytoflow.utility.logicle_scale)
LogicleMinorLocator (class in cytoflow.utility.logicle_scale)
LogicleScale (class in cytoflow.utility.logicle_scale)
LogScale (class in cytoflow.utility.log_scale)
low (cytoflow.operations.range.RangeOp attribute)
M
M (cytoflow.utility.logicle_scale.LogicleScale attribute)
main() (in module cytoflow.scripts.channel_voltages)
(in module cytoflow.scripts.fcs_metadata)
MatplotlibHlogScale (class in cytoflow.utility.hlog_scale)
MatplotlibHlogScale.HlogTransform (class in cytoflow.utility.hlog_scale)
MatplotlibHlogScale.InvertedLogicleTransform (class in cytoflow.utility.hlog_scale)
MatplotlibLogicleScale (class in cytoflow.utility.logicle_scale)
MatplotlibLogicleScale.InvertedLogicleTransform (class in cytoflow.utility.logicle_scale)
MatplotlibLogicleScale.LogicleTransform (class in cytoflow.utility.logicle_scale)
max_quantile (cytoflow.operations.density.DensityGateOp attribute)
merge_dist (cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
mesh_size (cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp attribute)
metadata (cytoflow.experiment.Experiment attribute)
min_quantile (cytoflow.operations.density.DensityGateOp attribute)
mixture_model (cytoflow.operations.color_translation.ColorTranslationOp attribute)
MplFilter (class in cytoflow)
N
name (cytoflow.operations.binning.BinningOp attribute)
(cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.color_translation.ColorTranslationDiagnostic attribute)
(cytoflow.operations.density.DensityGateOp attribute)
(cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
(cytoflow.operations.frame_stat.FrameStatisticOp attribute)
(cytoflow.operations.gaussian.GaussianMixtureOp attribute)
(cytoflow.operations.i_operation.IOperation attribute)
(cytoflow.operations.kmeans.KMeansOp attribute)
(cytoflow.operations.pca.PCAOp attribute)
(cytoflow.operations.polygon.PolygonOp attribute)
(cytoflow.operations.quad.QuadOp attribute)
(cytoflow.operations.range.RangeOp attribute)
(cytoflow.operations.range2d.Range2DOp attribute)
(cytoflow.operations.ratio.RatioOp attribute)
(cytoflow.operations.threshold.ThresholdOp attribute)
(cytoflow.operations.xform_stat.TransformStatisticOp attribute)
(cytoflow.utility.hlog_scale.HlogScale attribute)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale attribute)
(cytoflow.utility.linear_scale.LinearScale attribute)
(cytoflow.utility.log_scale.LogScale attribute)
(cytoflow.utility.logicle_scale.LogicleScale attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale attribute)
(cytoflow.utility.scale.IScale attribute)
name_metadata (cytoflow.operations.import_op.ImportOp attribute)
new_axes() (cytoflow.utility.matplotlib_widgets.SpanSelector method)
norm() (cytoflow.utility.hlog_scale.HlogScale method)
(cytoflow.utility.linear_scale.LinearScale method)
(cytoflow.utility.log_scale.LogScale method)
(cytoflow.utility.logicle_scale.LogicleScale method)
(cytoflow.utility.scale.IScale method)
NullView (class in cytoflow.operations.base_op_views)
num_clusters (cytoflow.operations.kmeans.KMeansOp attribute)
num_components (cytoflow.operations.gaussian.GaussianMixtureOp attribute)
(cytoflow.operations.pca.PCAOp attribute)
num_hist_bins() (in module cytoflow.utility.util_functions)
num_knots (cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseOp attribute)
numerator (cytoflow.operations.ratio.RatioOp attribute)
O
onmove() (cytoflow.utility.matplotlib_widgets.Cursor method)
(cytoflow.utility.matplotlib_widgets.PolygonSelector method)
onpress() (cytoflow.utility.matplotlib_widgets.PolygonSelector method)
op (cytoflow.operations.autofluorescence.AutofluorescenceDiagnosticView attribute)
(cytoflow.operations.base_op_views.OpView attribute)
(cytoflow.operations.bead_calibration.BeadCalibrationDiagnostic attribute)
(cytoflow.operations.binning.BinningView attribute)
(cytoflow.operations.bleedthrough_linear.BleedthroughLinearDiagnostic attribute)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseDiagnostic attribute)
(cytoflow.operations.color_translation.ColorTranslationDiagnostic attribute)
(cytoflow.operations.density.DensityGateView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DDensityView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks2DView attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.gaussian.GaussianMixture2DView attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.kmeans.KMeans2DView attribute)
(cytoflow.operations.polygon.PolygonSelection attribute)
(cytoflow.operations.quad.QuadSelection attribute)
(cytoflow.operations.range.RangeSelection attribute)
(cytoflow.operations.range2d.RangeSelection2D attribute)
(cytoflow.operations.threshold.ThresholdSelection attribute)
Op1DView (class in cytoflow.operations.base_op_views)
Op2DView (class in cytoflow.operations.base_op_views)
OpView (class in cytoflow.operations.base_op_views)
output_dims (cytoflow.utility.hlog_scale.MatplotlibHlogScale.HlogTransform attribute)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.InvertedLogicleTransform attribute)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.LogicleTransform attribute)
P
ParallelCoordinatesView (class in cytoflow.views.parallel_coords)
parse_tube() (in module cytoflow.operations.import_op)
path (cytoflow.views.export_fcs.ExportFCS attribute)
PCAOp (class in cytoflow.operations.pca)
percentiles() (in module cytoflow.utility.algorithms)
plot() (cytoflow.operations.autofluorescence.AutofluorescenceDiagnosticView method)
(cytoflow.operations.base_op_views.AnnotatingView method)
(cytoflow.operations.base_op_views.ByView method)
(cytoflow.operations.bead_calibration.BeadCalibrationDiagnostic method)
(cytoflow.operations.binning.BinningView method)
(cytoflow.operations.bleedthrough_linear.BleedthroughLinearDiagnostic method)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseDiagnostic method)
(cytoflow.operations.color_translation.ColorTranslationDiagnostic method)
(cytoflow.operations.density.DensityGateView method)
(cytoflow.operations.flowpeaks.FlowPeaks1DView method)
(cytoflow.operations.flowpeaks.FlowPeaks2DDensityView method)
(cytoflow.operations.flowpeaks.FlowPeaks2DView method)
(cytoflow.operations.gaussian.GaussianMixture1DView method)
(cytoflow.operations.gaussian.GaussianMixture2DView method)
(cytoflow.operations.kmeans.KMeans1DView method)
(cytoflow.operations.kmeans.KMeans2DView method)
(cytoflow.operations.polygon.PolygonSelection method)
(cytoflow.operations.quad.QuadSelection method)
(cytoflow.operations.range.RangeSelection method)
(cytoflow.operations.range2d.RangeSelection2D method)
(cytoflow.operations.threshold.ThresholdSelection method)
(cytoflow.views.bar_chart.BarChartView method)
(cytoflow.views.base_views.Base1DStatisticsView method)
(cytoflow.views.base_views.Base1DView method)
(cytoflow.views.base_views.Base2DStatisticsView method)
(cytoflow.views.base_views.Base2DView method)
(cytoflow.views.base_views.BaseDataView method)
(cytoflow.views.base_views.BaseNDView method)
(cytoflow.views.base_views.BaseStatisticsView method)
(cytoflow.views.base_views.BaseView method)
(cytoflow.views.densityplot.DensityView method)
(cytoflow.views.histogram.HistogramView method)
(cytoflow.views.histogram_2d.Histogram2DView method)
(cytoflow.views.i_view.IView method)
(cytoflow.views.kde_1d.Kde1DView method)
(cytoflow.views.kde_2d.Kde2DView method)
(cytoflow.views.parallel_coords.ParallelCoordinatesView method)
(cytoflow.views.radviz.RadvizView method)
(cytoflow.views.scatterplot.ScatterplotView method)
(cytoflow.views.stats_1d.Stats1DView method)
(cytoflow.views.stats_2d.Stats2DView method)
(cytoflow.views.table.TableView method)
(cytoflow.views.violin.ViolinPlotView method)
poly_area() (in module cytoflow.operations.gaussian)
PolygonOp (class in cytoflow.operations.polygon)
PolygonSelection (class in cytoflow.operations.polygon)
PolygonSelector (class in cytoflow.utility.matplotlib_widgets)
PositiveCFloat (class in cytoflow.utility.custom_traits)
PositiveCInt (class in cytoflow.utility.custom_traits)
PositiveFloat (class in cytoflow.utility.custom_traits)
PositiveInt (class in cytoflow.utility.custom_traits)
posteriors (cytoflow.operations.gaussian.GaussianMixtureOp attribute)
Q
QuadOp (class in cytoflow.operations.quad)
QuadSelection (class in cytoflow.operations.quad)
query() (cytoflow.experiment.Experiment method)
R
r (cytoflow.utility.logicle_scale.LogicleScale attribute)
RadvizView (class in cytoflow.views.radviz)
random_string() (in module cytoflow.utility.util_functions)
Range2DOp (class in cytoflow.operations.range2d)
RangeOp (class in cytoflow.operations.range)
RangeSelection (class in cytoflow.operations.range)
RangeSelection2D (class in cytoflow.operations.range2d)
RatioOp (class in cytoflow.operations.ratio)
register_scale() (in module cytoflow.utility.scale)
Removed (class in cytoflow.utility.custom_traits)
REMOVED_ERROR (cytoflow.views.base_views.Base1DStatisticsView attribute)
S
sanitize_identifier() (in module cytoflow.utility.util_functions)
scale (cytoflow.operations.base_op_views.Op1DView attribute)
(cytoflow.operations.binning.BinningOp attribute)
(cytoflow.operations.binning.BinningView attribute)
(cytoflow.operations.flowpeaks.FlowPeaks1DView attribute)
(cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
(cytoflow.operations.gaussian.GaussianMixture1DView attribute)
(cytoflow.operations.gaussian.GaussianMixtureOp attribute)
(cytoflow.operations.kmeans.KMeans1DView attribute)
(cytoflow.operations.kmeans.KMeansOp attribute)
(cytoflow.operations.pca.PCAOp attribute)
(cytoflow.operations.range.RangeSelection attribute)
(cytoflow.operations.threshold.ThresholdSelection attribute)
(cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.Base1DStatisticsView attribute)
(cytoflow.views.base_views.Base1DView attribute)
(cytoflow.views.base_views.BaseNDView attribute)
(cytoflow.views.histogram.HistogramView attribute)
(cytoflow.views.kde_1d.Kde1DView attribute)
(cytoflow.views.parallel_coords.ParallelCoordinatesView attribute)
(cytoflow.views.radviz.RadvizView attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
(cytoflow.views.violin.ViolinPlotView attribute)
scale_factory() (in module cytoflow.utility.scale)
ScaleEnum (class in cytoflow.utility.custom_traits)
ScaleMixin (class in cytoflow.utility.scale)
ScatterplotView (class in cytoflow.views.scatterplot)
set() (cytoflow.utility.custom_traits.Deprecated method)
(cytoflow.utility.custom_traits.Removed method)
set_default_locators_and_formatters() (cytoflow.utility.hlog_scale.MatplotlibHlogScale method)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale method)
set_default_scale() (in module cytoflow.utility.scale)
set_params() (cytoflow.utility.hlog_scale.HlogMajorLocator method)
(cytoflow.utility.hlog_scale.HlogMinorLocator method)
(cytoflow.utility.logicle_scale.LogicleMajorLocator method)
(cytoflow.utility.logicle_scale.LogicleMinorLocator method)
sigma (cytoflow.operations.density.DensityGateOp attribute)
(cytoflow.operations.gaussian.GaussianMixtureOp attribute)
SpanSelector (class in cytoflow.utility.matplotlib_widgets)
spillover (cytoflow.operations.bleedthrough_linear.BleedthroughLinearOp attribute)
statistic (cytoflow.operations.xform_stat.TransformStatisticOp attribute)
(cytoflow.utility.logicle_scale.LogicleScale attribute)
(cytoflow.utility.scale.IScale attribute)
(cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.Base1DStatisticsView attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
(cytoflow.views.table.TableView attribute)
statistic_name (cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.frame_stat.FrameStatisticOp attribute)
(cytoflow.operations.xform_stat.TransformStatisticOp attribute)
statistics (cytoflow.experiment.Experiment attribute)
Stats1DView (class in cytoflow.views.stats_1d)
Stats2DView (class in cytoflow.views.stats_2d)
STATS_REMOVED (cytoflow.views.base_views.Base2DStatisticsView attribute)
subset (cytoflow.operations.bleedthrough_linear.BleedthroughLinearDiagnostic attribute)
(cytoflow.operations.bleedthrough_piecewise.BleedthroughPiecewiseDiagnostic attribute)
(cytoflow.operations.channel_stat.ChannelStatisticOp attribute)
(cytoflow.operations.color_translation.ColorTranslationDiagnostic attribute)
(cytoflow.operations.frame_stat.FrameStatisticOp attribute)
(cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.BaseStatisticsView attribute)
(cytoflow.views.export_fcs.ExportFCS attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
(cytoflow.views.stats_2d.Stats2DView attribute)
(cytoflow.views.table.TableView attribute)
subset() (cytoflow.experiment.Experiment method)
T
TableView (class in cytoflow.views.table)
threshold (cytoflow.operations.threshold.ThresholdOp attribute)
ThresholdOp (class in cytoflow.operations.threshold)
ThresholdSelection (class in cytoflow.operations.threshold)
tick_values() (cytoflow.utility.hlog_scale.HlogMajorLocator method)
(cytoflow.utility.hlog_scale.HlogMinorLocator method)
(cytoflow.utility.logicle_scale.LogicleMajorLocator method)
(cytoflow.utility.logicle_scale.LogicleMinorLocator method)
tol (cytoflow.operations.flowpeaks.FlowPeaksOp attribute)
transform_non_affine() (cytoflow.utility.hlog_scale.MatplotlibHlogScale.HlogTransform method)
(cytoflow.utility.hlog_scale.MatplotlibHlogScale.InvertedLogicleTransform method)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.InvertedLogicleTransform method)
(cytoflow.utility.logicle_scale.MatplotlibLogicleScale.LogicleTransform method)
TransformStatisticOp (class in cytoflow.operations.xform_stat)
Tube (class in cytoflow.operations.import_op)
tubes (cytoflow.operations.import_op.ImportOp attribute)
U
units (cytoflow.operations.bead_calibration.BeadCalibrationOp attribute)
V
validate() (cytoflow.utility.custom_traits.CFloatOrNone method)
(cytoflow.utility.custom_traits.CIntOrNone method)
(cytoflow.utility.custom_traits.FloatOrNone method)
(cytoflow.utility.custom_traits.IntOrNone method)
(cytoflow.utility.custom_traits.PositiveCFloat method)
(cytoflow.utility.custom_traits.PositiveCInt method)
(cytoflow.utility.custom_traits.PositiveFloat method)
(cytoflow.utility.custom_traits.PositiveInt method)
variable (cytoflow.views.bar_chart.BarChartView attribute)
(cytoflow.views.base_views.BaseStatisticsView attribute)
(cytoflow.views.stats_1d.Stats1DView attribute)
(cytoflow.views.stats_2d.Stats2DView attribute)
(cytoflow.views.violin.ViolinPlotView attribute)
variable_scale (cytoflow.views.stats_1d.Stats1DView attribute)
vertices (cytoflow.operations.polygon.PolygonOp attribute)
view_limits() (cytoflow.utility.hlog_scale.HlogMajorLocator method)
(cytoflow.utility.logicle_scale.LogicleMajorLocator method)
(cytoflow.utility.logicle_scale.LogicleMinorLocator method)
ViolinPlotView (class in cytoflow.views.violin)
W
W (cytoflow.utility.logicle_scale.LogicleScale attribute)
whiten (cytoflow.operations.pca.PCAOp attribute)
write_fcs() (in module cytoflow.utility.fcswrite)
X
xchannel (cytoflow.operations.density.DensityGateOp attribute)
(cytoflow.operations.quad.QuadOp attribute)
(cytoflow.operations.range2d.Range2DOp attribute)
xhigh (cytoflow.operations.range2d.Range2DOp attribute)
xlow (cytoflow.operations.range2d.Range2DOp attribute)
xscale (cytoflow.operations.density.DensityGateOp attribute)
xthreshold (cytoflow.operations.quad.QuadOp attribute)
Y
ychannel (cytoflow.operations.density.DensityGateOp attribute)
(cytoflow.operations.quad.QuadOp attribute)
(cytoflow.operations.range2d.Range2DOp attribute)
yhigh (cytoflow.operations.range2d.Range2DOp attribute)
ylow (cytoflow.operations.range2d.Range2DOp attribute)
yscale (cytoflow.operations.density.DensityGateOp attribute)
ythreshold (cytoflow.operations.quad.QuadOp attribute)
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