\name{rectangleGate-class} \docType{class} \alias{rectangleGate-class} \alias{rectangleGate} \alias{summary,rectangleGate-method} \alias{show,rectangleGate-method} \alias{[,rectangleGate,character-method} \alias{[,rectangleGate,ANY-method} \alias{*,rectangleGate,rectangleGate-method} \title{Class "rectangleGate"} \description{ Class and constructor for n-dimensional rectangular \code{\linkS4class{filter}} objects. } \section{Extends}{ Class \code{"\linkS4class{parameterFilter}"}, directly. Class \code{"\linkS4class{concreteFilter}"}, by class \code{parameterFilter}, distance 2. Class \code{"\linkS4class{filter}"}, by class \code{parameterFilter}, distance 3. } \section{Slots}{ \describe{ \item{\code{min,max}:}{Objects of class \code{"numeric"}. The minimum and maximum values of the n-dimensional rectangular region. } \item{\code{parameters}:}{Object of class \code{"character"}, indicating the parameters for which the \code{rectangleGate} is defined.} \item{\code{filterId}:}{Object of class \code{"character"}, referencing the filter.} } } \section{Objects from the Class}{ Objects can be created by calls of the form \code{new("rectangleGate", ...)}, by using the constructor \code{rectangleGate} or by combining existing \code{rectangleGates} using the \code{*} method. Using the constructor is the recommended way of object instantiation: } \usage{ rectangleGate(\dots, .gate, filterId="defaultRectangleGate") } \arguments{ \item{filterId}{ An optional parameter that sets the \code{filterId} of this gate. The object can later be identified by this name.} \item{.gate}{ A definition of the gate. This can be either a list, or a matrix, as described below. } \item{\dots}{ You can also directly provide the boundaries of a \code{rectangleGate} as additional named arguments, as described below. } } \value{ Returns a \code{\link{rectangleGate}} object for use in filtering \code{\link{flowFrame}}s or other flow cytometry objects. } \section{Methods}{ \describe{ \item{\%in\%}{\code{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 \code{\link{filter}} methods. } \item{show}{\code{signature(object = "rectangleGate")}: Print information about the filter. } \item{*}{\code{signature(e1 = "rectangleGate", e2 = "rectangleGate")}: combining two \code{rectangleGates} into one higher dimensional representation. } \item{\[}{\code{signature(x = "rectangleGate", i = "character")}: Subsetting of a \code{rectangleGate} by parameter name(s). This is essentially the inverse to \code{*}. } } } \details{ This class describes a rectangular region in n dimensions, which is a Cartesian product of \code{n} orthogonal intervals in these dimensions. \code{n=1} corresponds to a range gate, \code{n=2} to a rectangle gate, \code{n=3} corresponds to a box region and \code{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 \code{Inf} or \code{-Inf}, repsectively. \code{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 \code{n} columns and \code{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 \code{rectangleGate} can be given as additional named arguments, where each of these arguments should be a numeric vector of length \code{2}; the function tries to collapse these boundary values into a matrix. Note that boundaries of \code{rectangleGates} where \code{min > max} are syntactically valid, however when evaluated they will always be empty. \code{rectangleGate} objects can also be multiplied using the \code{*} operator, provided that both gates have orthogonal axes. This results in higher-dimensional \code{rectangleGates}. The inverse operation of subsetting by parameter name(s) is also available. Evaluating a \code{rectangleGate} generates an object of class \code{\linkS4class{logicalFilterResult}}. Accordingly, \code{rectangleGates} can be used to subset and to split flow cytometry data sets. } \note{ See the documentation in the \code{\link[flowViz:flowViz-package]{flowViz}} package for details on plotting of \code{rectangleGates}. } \author{F.Hahne, B. Ellis N. Le Meur} \seealso{ \code{\link{flowFrame}}, \code{\link{polygonGate}}, \code{\link{ellipsoidGate}}, \code{\link{polytopeGate}}, \code{\link{filter}} for evaluation of \code{rectangleGates} and \code{\link{split}} and \code{\link{Subset}}for splitting and subsetting of flow cytometry data sets based on that. } \examples{ ## 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"] } \keyword{methods} \keyword{classes}