flowCore (version 1.38.2)

view-class: Class "view"

Description

Class and method to capture the results of standard operations (called "views" here) in a flow cytometry workflow.

Usage

view(workflow, ID=paste("viewRef", guid(), sep="_"), name="default", data, action)
parent(object)
Data(object)
action(object)
alias(object, ...)

Arguments

workflow

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

object

An object of class view or one of its subclasses.

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

References to the data and actionItem objects, respectively.

...

Further arguments that get passed to the generic.

Value

A reference to the view that is created inside the workFlow environment as a side effect of calling the constructor.The parent view (i.e., the view based on which the current view was created) for the parent method.

Objects from the Class

Objects should be created using the constructor view, which also assigns the view to a workFlow object.

Slots

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.

alias:

Object of class "fcAliasReference". A reference to the alias table.

data:

Object of class "fcDataReference" A reference to the data that is associated to the view. See gateView for details on copying and subsetting of the raw data in the context of gating.

Methods

action

signature(object = "view"): Accessor for the action slot. Note that this returns the actual actionItem object, i.e., the reference gets resolved.

Data

signature(object = "view"): Accessor for the data slot. Note that this returns the actual data object, i.e., the reference gets resolved.

names

signature(x = "view"): Accessor to the name slot.

alias

signature(object = "view"): Get the alias table from a view.

parent

signature(object = "view"): The parent view, i.e., the view based on which the current view was created.

print

signature(x = "view"): Print details about the object.

Rm

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

show

signature(object = "view"): Print details about the object.

xyplot

signature(x = "formula", data = "view"): Plot the data underlying the view.

xyplot

signature(x = "view", data = "missing"): Plot the data underlying the view.

Details

Views provide a means to bind the results of standard operations on flow cytometry data in a workflow. Each view can be considered the outcome of one operation. There are more specific subclasses for the three possible types of operation: gateView for gating operations, transformView for transformations, and compensateView for compensation operations. See their documentation for details.

See Also

workFlow, gateView, transformView, compensateView, actionItem

Examples

showClass("view")