cytoflow.operations.range2d

Applies a 2D range gate (ie, a rectangle gate) to an Experiment. range2d has two classes:

Range2DOp – Applies the gate, given four thresholds

ScatterplotRangeSelection2DView – an IView that allows you to view the range and/or interactively set the thresholds on a scatterplot.

DensityRangeSelection2DView – an IView that allows you to view the range and/or interactively set the thresholds on a scatterplot.

class cytoflow.operations.range2d.Range2DOp

Bases: traits.has_traits.HasStrictTraits

Apply a 2D range gate to a cytometry experiment.

name

The operation name. Used to name the new metadata field in the experiment that’s created by apply

Type

Str

xchannel

The name of the first channel to apply the range gate.

Type

Str

xlow

The lowest value in xchannel to include in this gate.

Type

Float

xhigh

The highest value in xchannel to include in this gate.

Type

Float

ychannel

The name of the second channel to apply the range gate.

Type

Str

ylow

The lowest value in ychannel to include in this gate.

Type

Float

yhigh

The highest value in ychannel to include in this gate.

Type

Float

Examples

Make a little data set.

>>> import cytoflow as flow
>>> import_op = flow.ImportOp()
>>> import_op.tubes = [flow.Tube(file = "Plate01/RFP_Well_A3.fcs",
...                              conditions = {'Dox' : 10.0}),
...                    flow.Tube(file = "Plate01/CFP_Well_A4.fcs",
...                              conditions = {'Dox' : 1.0})]
>>> import_op.conditions = {'Dox' : 'float'}
>>> ex = import_op.apply()

Create and parameterize the operation.

>>> r = flow.Range2DOp(name = "Range2D",
...                    xchannel = "V2-A",
...                    xlow = 10,
...                    xhigh = 1000,
...                    ychannel = "Y2-A",
...                    ylow = 1000,
...                    yhigh = 20000)

Show the default view.

>>> rv = r.default_view(huefacet = "Dox",
...                     xscale = 'log',
...                     yscale = 'log')

>>> rv.plot(ex)

Note

If you want to use the interactive default view in a Jupyter notebook, make sure you say %matplotlib notebook in the first cell (instead of %matplotlib inline or similar). Then call default_view() with interactive = True:

rv = r.default_view(huefacet = "Dox",
                    xscale = 'log',
                    yscale = 'log',
                    interactive = True)
rv.plot(ex)

Apply the gate, and show the result

>>> ex2 = r.apply(ex)
>>> ex2.data.groupby('Range2D').size()
Range2D
False    16405
True      3595
dtype: int64

apply(experiment)

Applies the threshold to an experiment.

Parameters

experiment (Experiment) – the Experiment to which this op is applied

Returns

a new Experiment, the same as the old experiment but with a new column with a data type of bool and the same as the operation name. The bool is True if the event’s measurement in xchannel is greater than xlow and less than xhigh, and the event’s measurement in ychannel is greater than ylow and less than yhigh; it is False otherwise.

Return type

Experiment

default_view(**kwargs)

Returns an IView that allows a user to view the selection or interactively draw it.

Parameters

density (bool, default = False) – If True, return a density plot instead of a scatterplot.

class cytoflow.operations.range2d.ScatterplotRangeSelection2DView

Bases: cytoflow.operations.range2d._RangeSelection2D, cytoflow.views.scatterplot.ScatterplotView

Plots, and lets the user interact with, a 2D selection.

interactive

is this view interactive? Ie, can the user set min and max with a mouse drag?

Type

Bool

xchannel

The channels to use for this view’s X axis. If you created the view using default_view, this is already set.

Type

Str

ychannel

The channels to use for this view’s Y axis. If you created the view using default_view, this is already set.

Type

Str

xscale

The way to scale the x axis. If you created the view using default_view, this may be already set.

Type

{‘linear’, ‘log’, ‘logicle’}

yscale

The way to scale the y axis. If you created the view using default_view, this may be already set.

Type

{‘linear’, ‘log’, ‘logicle’}

op

The IOperation that this view is associated with. If you created the view using default_view, this is already set.

Type

Instance(IOperation)

subset

An expression that specifies the subset of the statistic to plot. Passed unmodified to pandas.DataFrame.query.

Type

str

xfacet

Set to one of the Experiment.conditions in the Experiment, and a new column of subplots will be added for every unique value of that condition.

Type

String

yfacet

Set to one of the Experiment.conditions in the Experiment, and a new row of subplots will be added for every unique value of that condition.

Type

String

huefacet

Set to one of the Experiment.conditions in the in the Experiment, and a new color will be added to the plot for every unique value of that condition.

Type

String

huescale

How should the color scale for huefacet be scaled?

Type

{‘linear’, ‘log’, ‘logicle’}

Examples

In a Jupyter notebook with %matplotlib notebook

>>> r = flow.Range2DOp(name = "Range2D",
...                    xchannel = "V2-A",
...                    ychannel = "Y2-A"))
>>> rv = r.default_view()
>>> rv.interactive = True
>>> rv.plot(ex2)

class cytoflow.operations.range2d.DensityRangeSelection2DView

Bases: cytoflow.operations.range2d._RangeSelection2D, cytoflow.views.densityplot.DensityView

Plots, and lets the user interact with, a 2D selection.

interactive

is this view interactive? Ie, can the user set min and max with a mouse drag?

Type

Bool

xchannel

The channels to use for this view’s X axis. If you created the view using default_view, this is already set.

Type

Str

ychannel

The channels to use for this view’s Y axis. If you created the view using default_view, this is already set.

Type

Str

xscale

The way to scale the x axis. If you created the view using default_view, this may be already set.

Type

{‘linear’, ‘log’, ‘logicle’}

yscale

The way to scale the y axis. If you created the view using default_view, this may be already set.

Type

{‘linear’, ‘log’, ‘logicle’}

op

The IOperation that this view is associated with. If you created the view using default_view, this is already set.

Type

Instance(IOperation)

huefacet

You must leave the hue facet unset!

Type

None

subset

An expression that specifies the subset of the statistic to plot. Passed unmodified to pandas.DataFrame.query.

Type

str

xfacet

Set to one of the Experiment.conditions in the Experiment, and a new column of subplots will be added for every unique value of that condition.

Type

String

yfacet

Set to one of the Experiment.conditions in the Experiment, and a new row of subplots will be added for every unique value of that condition.

Type

String

huescale

How should the color scale for huefacet be scaled?

Type

{‘linear’, ‘log’, ‘logicle’}

Examples

In a Jupyter notebook with %matplotlib notebook

>>> r = flow.Range2DOp(name = "Range2D",
...                    xchannel = "V2-A",
...                    ychannel = "Y2-A"))
>>> rv = r.default_view(density = True)
>>> rv.interactive = True
>>> rv.plot(ex2)