gateView-class: Class "gateView"

Description Usage Arguments Details Value Objects from the Class Slots Extends Methods Author(s) See Also Examples

Description

Class and method to capture the result of gating operations in a flow cytometry workflow.

Usage

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gateView(workflow, ID=paste("gateViewRef", guid(), sep="_"),
                     name="default", action, data, indices, 
                     filterResult, frEntry)

Arguments

workflow

An object of class workFlow for which a view is to be created.

ID

A unique identifier of the view, most likely created by using the internal guid function.

name

A more human-readable name of the view.

data, action, filterResult

References to the data, filterResult, and actionItem objects, respectively.

indices

A logical vector of indices in the parent data.

frEntry

A character vector indicating the name of the population in the filterResult.

Details

gateViews provide a means to bind the results of gating operations in a workflow. Each gateView represents one of the populations that arise from the gating. logicalFilterResults create two gateViews (events in the gate and events not in the gate), multipleFilterResults one view for each population. See the documentation of the parent class view for more details.

Value

A reference to the gateView that is created inside the workFlow environment as a side effect of calling the add method.

A gateView object for the constructor.

Objects from the Class

Objects should be created using the add method, which creates a gateView from a filter object and directly assigns it to a workFlow. Alternatively, one can use the gateView constructor function for more programmatic access.

Slots

indices:

Object of class "logical". The indices in the parent data for events that are within the filter.

filterResult:

Object of class "fcFilterResultReference". A reference to the outcome of the filtering operation.

frEntry:

Object of class "character" The population in the filterResult that corresponds to the current view. See details for further explanation.

ID:

Object of class "character". A unique identifier for the view.

name:

Object of class "character". A more human-readable name

action:

Object of class "fcActionReference". A reference to the actionItem that generated the view.

env:

Object of class "environment". The evaluation environment in the workFlow.

data:

Object of class "fcDataReference" A reference to the data that is associated to the view. Subsets of the data are only generated when a a further action is invoked on a particular gateView. Summary statistics about the view can be acquired through the usual process of summarizing filterResults.

Extends

Class "view", directly.

Methods

Rm

signature(symbol = "gateView", envir = "workFlow", subSymbol = "character"): Remove a gateView from a workFlow. This method is recursive and will also remove all dependent views and actionItems.

summary

signature(x = "formula", data = "gateView"): Summarize the gating operation.

xyplot

signature(x = "formula", data = "gateView"): Plot the data of the gateView along with the gate.

Author(s)

Florian Hahne

See Also

workFlow, view, transformView, compensateView, actionItem

Examples

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showClass("view")

Bioconductor-mirror/flowCore documentation built on July 7, 2017, 11:55 p.m.