Class "GatingSet"

Description

GatingSet holds a set of GatingHierarchy objects, representing a set of samples and the gating scheme associated with each.

[ subsets a GatingSet or GatingSetList using the familiar bracket notation

[[ extract a GatingHierarchy object from a GatingSet or GatingSetList

Usage

## S4 method for signature 'GatingSetList,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'GatingSet,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'GatingSet,numeric'
x[[i, j, ...]]

Arguments

Details

Objects stores a collection of GatingHierarchies and represent a group in a flowJo workspace. A GatingSet can have two “states”. After a call to parseWorkspace(...,execute=FALSE) , the workspace is imported but the data is not. Setting execute to TRUE is needed in order to load, transform, compensate, and gate the associated data. Whether or not a GatingHierarchy has been applied to data is encoded in the flag slot. Some methods will warn the user, or may not function correctly if the GatingHierarchy has not been executed. This mechanism is in place, largely for the purpose of speed when working with larger workspaces. It allows the use to load a workspace and subset desired samples before proceeding to load the data.

Slots

FCSPath:

deprecated

data:

Object of class "flowSet". flow data associated with this GatingSet

flag:

Object of class "logical". A flag indicating whether the gates, transformations, and compensation matrices have been applied to data, or simply imported.

axis:

Object of class "list". stores the axis information used for plotGate.

pointer:

Object of class "externalptr". points to the gating hierarchy stored in C data structure.

guid:

Object of class "character". the unique identifier for GatingSet object.

transformation:

Object of class "list". a list of transformation objects used by GatingSet.

compensation:

Object of class "ANY". compensation objects.

See Also

GatingHierarchy flowJoWorkspace parseWorkspace

Examples

require(flowWorkspaceData)
  d<-system.file("extdata",package="flowWorkspaceData")
  wsfile<-list.files(d,pattern="A2004Analysis.xml",full=TRUE)
  ws <- openWorkspace(wsfile);
  G<-try(parseWorkspace(ws,execute=TRUE,path=d,name=1));
  plotPopCV(G);

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(flowWorkspace)
Loading required package: flowCore
Loading required package: flowViz
Loading required package: lattice
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowWorkspace/GatingSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GatingSet-class
> ### Title: Class '"GatingSet"'
> ### Aliases: GatingSet-class [,GatingSet,ANY-method
> ###   [,GatingSetList,ANY-method [[,GatingSet,character-method
> ###   [[,GatingSet,logical-method [[,GatingSet,numeric-method
> 
> ### ** Examples
> 
> require(flowWorkspaceData)
Loading required package: flowWorkspaceData
>   d<-system.file("extdata",package="flowWorkspaceData")
>   wsfile<-list.files(d,pattern="A2004Analysis.xml",full=TRUE)
>   ws <- openWorkspace(wsfile);
>   G<-try(parseWorkspace(ws,execute=TRUE,path=d,name=1));
Parsing 2 samples
mac version of flowJo workspace recognized.
Creating ncdfFlowSet...
All FCS files have the same following channels:
FSC-A
FSC-H
FSC-W
SSC-A
SSC-H
SSC-W
Am Cyan-A
Am Cyan-H
Pacific Blue-A
Pacific Blue-H
APC-A
APC-H
APC-CY7-A
APC-CY7-H
Alexa 700-A
Alexa 700-H
FITC-A
FITC-H
PerCP-CY5-5-A
PerCP-CY5-5-H
PE-CY7-A
PE-CY7-H
Time
done!
loading data: /home/ddbj/local/lib64/R/library/flowWorkspaceData/extdata/a2004_O1T2pb05i_A1_A01.fcs
Compensating
gating ...
write a2004_O1T2pb05i_A1_A01.fcs_61832 to empty cdf slot...
loading data: /home/ddbj/local/lib64/R/library/flowWorkspaceData/extdata/a2004_O1T2pb05i_A2_A02.fcs
Compensating
gating ...
write a2004_O1T2pb05i_A2_A02.fcs_45363 to empty cdf slot...
done!
>   plotPopCV(G);
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>