cytoflowgui.workflow.operations.flowpeaks

class cytoflowgui.workflow.operations.flowpeaks.FlowPeaksWorkflowOp[source]

Bases: cytoflowgui.workflow.operations.operation_base.WorkflowOperation, cytoflow.operations.flowpeaks.FlowPeaksOp

default_view(**kwargs)[source]

Returns a diagnostic plot of the Gaussian mixture model.

Parameters

  • channels (List(Str)) – Which channels to plot? Must be contain either one or two channels.

  • scale (List({‘linear’, ‘log’, ‘logicle’})) – How to scale the channels before plotting them

  • density (bool) – Should we plot a scatterplot or the estimated density function?

Returns

an IView, call plot to see the diagnostic plot.

Return type

IView

estimate(experiment)[source]

Estimate the k-means clusters, then hierarchically merge them.

Parameters

  • experiment (Experiment) – The Experiment to use to estimate the k-means clusters

  • subset (str (default = None)) – A Python expression that specifies a subset of the data in experiment to use to parameterize the operation.

apply(experiment)[source]

Assign events to a cluster.

Assigns each event to one of the k-means centroids from estimate, then groups together events in the same cluster hierarchy.

Parameters

experiment (Experiment) – the Experiment to apply the gate to.

Returns

A new Experiment with the gate applied to it. TODO - document the extra statistics

Return type

Experiment

clear_estimate()[source]
get_notebook_code(idx)[source]
class cytoflowgui.workflow.operations.flowpeaks.FlowPeaksWorkflowView[source]

Bases: cytoflowgui.workflow.views.view_base.WorkflowByView, cytoflow.operations.base_op_views.By2DView

id = 'edu.mit.synbio.cytoflowgui.op_plugins.flowpeaks'
friendly_id = 'FlowPeaks'
plot(experiment, **kwargs)[source]

A default plot that passes current_plot as the plot name.

get_notebook_code(idx)[source]