rectangleGate-class: Class "rectangleGate"

Description

Class and constructor for n-dimensional rectangular filter objects.

Usage

rectangleGate(..., .gate, filterId="defaultRectangleGate")

Arguments

filterId

An optional parameter that sets the filterId of this gate. The object can later be identified by this name.

.gate

A definition of the gate. This can be either a list, or a matrix, as described below.

...

You can also directly provide the boundaries of a rectangleGate as additional named arguments, as described below.

Value

Returns a rectangleGate object for use in filtering flowFrames or other flow cytometry objects.

Extends

Class "parameterFilter", directly. Class "concreteFilter", by class parameterFilter, distance 2. Class "filter", by class parameterFilter, distance 3.

Slots

min,max:: Objects of class "numeric". The minimum and maximum values of the n-dimensional rectangular region.
parameters:: Object of class "character", indicating the parameters for which the rectangleGate is defined.
filterId:: Object of class "character", referencing the filter.

Objects from the Class

Objects can be created by calls of the form

new("rectangleGate",
    ...)

, by using the constructor rectangleGate or by combining existing rectangleGates using the * method. Using the constructor is the recommended way of object instantiation:

Methods

%in%: signature(x = "flowFrame", table = "rectangleGate"): The workhorse used to evaluate the filter on data. This is usually not called directly by the user, but internally by calls to the filter methods.
show: signature(object = "rectangleGate"): Print information about the filter.
*: signature(e1 = "rectangleGate", e2 = "rectangleGate"): combining two rectangleGates into one higher dimensional representation.
\[: signature(x = "rectangleGate", i = "character"): Subsetting of a rectangleGate by parameter name(s). This is essentially the inverse to *.

Details

This class describes a rectangular region in n dimensions, which is a Cartesian product of n orthogonal intervals in these dimensions. n=1 corresponds to a range gate, n=2 to a rectangle gate, n=3 corresponds to a box region and n>3 to a hyper-rectangular regions. Intervals may be open on one side, in which case the value for the boundary is supposed to be Inf or -Inf, respectively. rectangleGates are inclusive, that means that events on the boundaries are considered to be in the gate. The constructor is designed to be useful in both direct and programmatic usage. To use it programmatically, you may either construct a named list or you may construct a matrix with n columns and 2 rows. The first row corresponds to the minimal value for each parameter while the second row corresponds to the maximal value for each parameter. The names of the parameters are taken from the column names or from the list names, respectively. Alternatively, the boundaries of the rectangleGate can be given as additional named arguments, where each of these arguments should be a numeric vector of length 2; the function tries to collapse these boundary values into a matrix.

Note that boundaries of rectangleGates where min > max are syntactically valid, however when evaluated they will always be empty.

rectangleGate objects can also be multiplied using the * operator, provided that both gates have orthogonal axes. This results in higher-dimensional rectangleGates. The inverse operation of subsetting by parameter name(s) is also available.

Evaluating a rectangleGate generates an object of class logicalFilterResult. Accordingly, rectangleGates can be used to subset and to split flow cytometry data sets.

Examples

Run this code


## Loading example data
dat <- read.FCS(system.file("extdata","0877408774.B08",
package="flowCore"))

#Create directly. Most likely from a command line
rectangleGate(filterId="myRectGate", "FSC-H"=c(200, 600), "SSC-H"=c(0, 400))

#To facilitate programmatic construction we also have the following
rg <- rectangleGate(filterId="myRectGate", list("FSC-H"=c(200, 600),
"SSC-H"=c(0, 400)))
mat <- matrix(c(200, 600, 0, 400), ncol=2, dimnames=list(c("min", "max"),
c("FSC-H", "SSC-H")))
rg <- rectangleGate(filterId="myRectGate", .gate=mat)

## Filtering using rectangleGates
fres <- filter(dat, rg)
fres
summary(fres)

## The result of rectangle filtering is a logical subset
Subset(dat, fres)

## We can also split, in which case we get those events in and those
## not in the gate as separate populations
split(dat, fres)

## Multiply rectangle gates
rg1 <- rectangleGate(filterId="FSC-", "FSC-H"=c(-Inf, 50))
rg2 <- rectangleGate(filterId="SSC+", "SSC-H"=c(50, Inf))
rg1 * rg2

## Subset rectangle gates
rg["FSC-H"]

##2d rectangleGate can be coerced to polygonGate
as(rg, "polygonGate")

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