\name{flowFrame-class} \docType{class} \alias{flowFrame-class} \alias{flowFrame} \alias{[,flowFrame,ANY-method} \alias{[,flowFrame,filter-method} \alias{[,flowFrame,filterResult-method} \alias{$.flowFrame} \alias{exprs} \alias{exprs<-} \alias{exprs,flowFrame-method} \alias{exprs<-,flowFrame,matrix-method} \alias{exprs<-,flowFrame,ANY-method} \alias{initialize,flowFrame-method} \alias{head,flowFrame-method} \alias{tail,flowFrame-method} \alias{description} \alias{description,flowFrame-method} \alias{description<-,flowFrame,list-method} \alias{description<-,flowFrame,ANY-method} \alias{show,flowFrame-method} \alias{plot,flowFrame,ANY-method} \alias{plot,flowFrame-method} \alias{summary,flowFrame-method} \alias{ncol} \alias{ncol,flowFrame-method} \alias{nrow} \alias{nrow,flowFrame-method} \alias{dim} \alias{dim,flowFrame-method} \alias{featureNames} \alias{featureNames,flowFrame-method} \alias{colnames} \alias{colnames,flowFrame-method} \alias{colnames<-} \alias{colnames<-,flowFrame-method} \alias{names} \alias{names,flowFrame-method} \alias{range} \alias{range,flowFrame-method} \alias{cbind2,flowFrame,matrix-method} \alias{cbind2,flowFrame,numeric-method} \alias{transform,flowFrame-method} \alias{compensate,flowFrame,matrix-method} \alias{compensate,flowFrame,data.frame-method} \alias{compensate,flowFrame,compensation-method} \alias{==,flowFrame,filterResult-method} \alias{==,flowFrame,flowFrame-method} \alias{<,flowFrame,ANY-method} \alias{<=,flowFrame,ANY-method} \alias{>,flowFrame,ANY-method} \alias{>=,flowFrame,ANY-method} \alias{spillover,flowFrame-method} \title{'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run } \description{This class represents the data contained in a \acronym{FCS} file or similar data structure. There are three parts of the data: \enumerate{ \item a numeric matrix of the raw measurement values with \kbd{rows=events} and \kbd{columns=parameters} \item annotation for the parameters (e.g., the measurement channels, stains, dynamic range) \item additional annotation provided through keywords in the \acronym{FCS} file } } \section{Creating Objects}{ Objects can be created using\cr \code{ new("flowFrame",}\cr \code{ exprs = ...., Object of class matrix}\cr \code{ parameters = ...., Object of class AnnotatedDataFrame}\cr \code{ description = ...., Object of class list}\cr \code{ )}\cr or the constructor \code{flowFrame}, with mandatory arguments \code{exprs} and optional arguments \code{parameters} and \code{description}. \code{flowFrame(exprs, parameters, description=list())} To create a \code{flowFrame} directly from an \acronym{FCS} file, use function \code{\link[flowCore]{read.FCS}}. This is the recommended and safest way of object creation, since \code{read.FCS} will perform basic data quality checks upon import. Unless you know exactly what you are doing, creating objects using \code{new} or the constructor is discouraged. } \section{Slots}{ \describe{ \item{\code{exprs}:}{Object of class \code{matrix} containing the measured intensities. Rows correspond to cells, columns to the different measurement channels. The \code{colnames} attribute of the matrix is supposed to hold the names or identifiers for the channels. The \code{rownames} attribute would usually not be set. } \item{\code{parameters}:}{An \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}} containing information about each column of the \code{flowFrame}. This will generally be filled in by \code{read.FCS} or similar functions using data from the \acronym{FCS} keywords describing the parameters.} \item{\code{description}:}{A list containing the meta data included in the FCS file.} } } \section{Methods}{ \describe{ There are separate documentation pages for most of the methods listed here which should be consulted for more details. \item{[}{Subsetting. Returns an object of class \code{flowFrame}. The subsetting is applied to the \code{exprs} slot, while the \code{description} slot is unchanged. The syntax for subsetting is similar to that of \code{\link[=data.frame]{data.frames}}. In addition to the usual index vectors (integer and logical by position, character by parameter names), \code{flowFrames} can be subset via \code{\link{filterResult}} and \code{\linkS4class{filter}} objects. \emph{Usage:} \code{ flowFrame[i,j]} \code{ flowFrame[filter,]} \code{ flowFrame[filterResult,]} Note that the value of argument \code{drop} is ignored when subsetting \code{flowFrames}. } \item{\$}{Subsetting by channel name. This is similar to subsetting of columns of \code{\link[=data.frame]{data.frames}}, i.e., \code{frame$FSC.H} is equivalent to \code{frame[, "FSC.H"]}. Note that column names may have to be quoted if they are no valid R symbols (e.g. \code{frame$"FSC-H"}). } \item{exprs, exprs<-}{Extract or replace the raw data intensities. The replacement value must be a numeric matrix with colnames matching the parameter definitions. Implicit subsetting is allowed (i.e. less columns in the replacement value compared to the original \code{flowFrame}, but all have to be defined there). \emph{Usage:} \code{ exprs(flowFrame)} \code{ exprs(flowFrame) <- value} } \item{head, tail}{Show first/last elements of the raw data matrix \emph{Usage:} \code{ head(flowFrame)} \code{ tail(flowFrame)} } \item{description, description<-}{Extract or replace the whole list of annotation keywords. Usually one would only be interested in a subset of keywords, in which case the \code{keyword} method is more appropriate. The optional \code{hideInternal} parameter can be used to exclude internal FCS parameters starting with\code{\\$}. \emph{Usage:} \code{ description(flowFrame)} \code{ description(flowFrame) <- value} } \item{keyword, keyword<-}{Extract ore replace one or more entries from the \code{description} slot by keyword. Methods are defined for character vectors (select a keyword by name), functions (select a keyword by evaluating a function on their content) and for lists (a combination of the above). See \code{\link{keyword}} for details. \emph{Usage:} \code{ keyword(flowFrame)} \code{ keyword(flowFrame, character)} \code{ keyword(flowFrame, list)} \code{ keyword(flowFrame) <- list(value) } } \item{parameters, parameters<-}{Extract parameters and return an object of class \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}}, or replace such an object. To access the actual parameter annotation, use \code{pData(parameters(frame))}. Replacement is only valid with \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrames}} containing all varLabels \code{name}, \code{desc}, \code{range}, \code{minRange} and \code{maxRange}, and matching entries in the \code{name} column to the colnames of the \code{exprs} matrix. See \code{\link{parameters}} for more details. \emph{Usage:} \code{ parameters(flowFrame)} \code{ parameters(flowFrame) <- value} } \item{show}{ Display details about the \code{flowFrame} object. } \item{summary}{Return descriptive statistical summary (min, max, mean and quantile) for each channel \emph{Usage:} \code{ summary(flowFrame)} } \item{plot}{Basic plots for \code{flowFrame} objects. If the object has only a single parameter this produces a \code{\link[graphics:hist]{histogram}}. For exactly two parameters we plot a bivariate density map (see \code{\link[graphics]{smoothScatter}} and for more than two parameters we produce a simple \code{\link[lattice]{splom}} plot. To select specific parameters from a \code{flowFrame} for plotting, either subset the object or specify the parameters as a character vector in the second argument to \code{plot}. The smooth parameters lets you toggle between density-type \code{\link[graphics]{smoothScatter}} plots and regular scatterplots. For far more sophisticated plotting of flow cytometry data, see the \code{\link[flowViz:flowViz-package]{flowViz}} package. \emph{Usage:} \code{ plot(flowFrame, ...)} \code{ plot(flowFrame, character, ...)} \code{ plot(flowFrame, smooth=FALSE, ...)} } \item{ncol, nrow, dim}{Extract the dimensions of the data matrix. \emph{Usage:} \code{ ncol(flowFrame)} \code{ nrow(flowFrame)} \code{ dim(flowFrame)} } \item{featureNames, colnames, colnames<-}{Extract parameter names (i.e., the colnames of the data matrix). \code{colnames} and \code{featureNames} are synonymes. For \code{colnames} there is also a replacement method. This will update the \code{name} column in the \code{parameters} slot as well. \emph{Usage:} \code{ featureNames(flowFrame)} \code{ colnames(flowFrame)} \code{ colnames(flowFrame) <- value} } \item{names}{Extract pretty formated names of the parameters including parameter descriptions. \emph{Usage:} \code{ names(flowFrame)} } \item{identifier}{Extract GUID of a \code{flowFrame}. Returns the file name if no GUID is available. See \code{\link{identifier}} for details. \emph{Usage:} \code{ identifier(flowFrame)} } \item{range}{Get dynamic range of the \code{flowFame}. Note that this is not necessarily the range of the actual data values, but the theoretical range of values the measurement instrument was able to capture. The values of the dynamic range will be transformed when using the transformation methods for \code{flowFrames}. Additional character arguments are evaluated as parameter names for which to return the dynamic range. \emph{Usage:} \code{ range(flowFrame, ...)} } \item{each\_row, each\_col}{Apply functions over rows or columns of the data matrix. These are convenince methods. See \code{\link{each_col}} for details. \emph{Usage:} \code{ each_row(flowFrame, function, ...)} \code{ each_col(flowFrame, function, ...)} } \item{transform}{Apply a transformation function on a \code{flowFrame} object. This uses R's \code{\link[base]{transform}} function by treating the \code{flowFrame} like a regular \code{data.frame}. \code{flowCore} provides an additional inline mechanism for transformations (see \code{\link{\%on\%}}) which is strictly more limited than the out-of-line transformation described here. \emph{Usage:} \code{ transform(flowFrame, ...)} } \item{filter}{Apply a \code{\linkS4class{filter}} object on a \code{flowFrame} object. This returns an object of class \code{\link{filterResult}}, which could then be used for subsetting of the data or to calculate summary statistics. See \code{\link{filter}} for details. \emph{Usage:} \code{ filter(flowFrame, filter)} } \item{split}{Split \code{flowFrame} object according to a \code{\link{filter}}, a \code{\link{filterResult}} or a \code{factor}. For most types of filters, an optional \code{flowSet=TRUE} parameter will create a \code{\linkS4class{flowSet}} rather than a simple list. See \code{\link{split}} for details. \emph{Usage:} \code{ split(flowFrame, filter, flowSet=FALSE, ...)} \code{ split(flowFrame, filterResult, flowSet=FALSE, ...)} \code{ split(flowFrame, factor, flowSet=FALSE, ...)} } \item{Subset}{Subset a \code{flowFrame} according to a \code{filter} or a logical vector. The same can be done using the standard subsetting operator with a \code{filter}, \code{filterResult}, or a logical vector as first argument. \emph{Usage:} \code{ Subset(flowFrame, filter)} \code{ Subset(flowFrame, logical)} } \item{cbind2}{Expand a \code{flowFrame} by the data in a \code{numeric matrix} of the same length. The \code{matrix} must have column names different from those of the \code{flowFrame}. The additional method for \code{numerics} only raises a useful error message. \emph{Usage:} \code{ cbind2(flowFrame, matrix)} \code{ cbind2(flowFrame, numeric)} } \item{compensate}{Apply a compensation matrix (or a \code{\linkS4class{compensation}} object) on a \code{flowFrame} object. This returns a compensared \code{flowFrame}. \emph{Usage:} \code{ compensate(flowFrame, matrix)} \code{ compensate(flowFrame, data.frame)} } \item{spillover}{Extract spillover matrix from description slot if present. \emph{Usage:} \code{ spillover(flowFrame, matrix)} } \item{==}{Test equality between two \code{flowFrames}} \item{<, >, <=, >=}{These operators basically treat the \code{flowFrame} as a numeric matrix.} \item{\code{initialize(flowFrame)}:}{Object instantiation, used by \code{new}; not to be called directly by the user.} } } \details{ Objects of class \code{flowFrame} can be used to hold arbitrary data of cell populations, acquired in flow-cytometry. \acronym{FCS} is the Data File Standard for Flow Cytometry, the current version is FCS 3.0. See the vignette of this package for additional information on using the object system for handling of flow-cytometry data. } \author{ F. Hahne, B. Ellis, P. Haaland and N. Le Meur } \seealso{ \code{\linkS4class{flowSet}}, \code{\link{read.FCS}} } \examples{ ## load example data data(GvHD) frame <- GvHD[[1]] ## subsetting frame[1:4,] frame[,3] frame[,"FSC-H"] frame$"SSC-H" ## accessing and replacing raw values head(exprs(frame)) exprs(frame) <- exprs(frame)[1:3000,] frame exprs(frame) <- exprs(frame)[,1:6] frame ## access FCS keywords head(description(frame)) keyword(frame, c("FILENAME", "$FIL")) ## parameter annotation parameters(frame) pData(parameters(frame)) ## summarize frame data summary(frame) ## plotting plot(frame) if(require(flowViz)){ plot(frame) plot(frame, c("FSC-H", "SSC-H")) plot(frame[,1]) plot(frame, c("FSC-H", "SSC-H"), smooth=FALSE) } ## frame dimensions ncol(frame) nrow(frame) dim(frame) ## accessing and replacing parameter names featureNames(frame) all(featureNames(frame) == colnames(frame)) colnames(frame) <- make.names(colnames(frame)) colnames(frame) parameters(frame)$name names(frame) ## accessing a GUID identifier(frame) identifier(frame) <- "test" ## dynamic range of a frame range(frame) range(frame, "FSC.H", "FL1.H") range(frame)$FSC.H ## iterators head(each_row(frame, mean)) head(each_col(frame, mean)) ## transformation opar <- par(mfcol=c(1:2)) if(require(flowViz)) plot(frame, c("FL1.H", "FL2.H")) frame <- transform(frame, FL1.H=log(`FL1.H`), FL2.H=log(`FL2.H`)) if(require(flowViz)) plot(frame, c("FL1.H", "FL2.H")) par(opar) range(frame) ## filtering of flowFrames rectGate <- rectangleGate(filterId="nonDebris","FSC.H"=c(200,Inf)) fres <- filter(frame, rectGate) summary(fres) ## splitting of flowFrames split(frame, rectGate) split(frame, rectGate, flowSet=TRUE) split(frame, fres) f <- cut(exprs(frame$FSC.H), 3) split(frame, f) ## subsetting according to filters and filter results Subset(frame, rectGate) Subset(frame, fres) Subset(frame, as.logical(exprs(frame$FSC.H) < 300)) frame[rectGate,] frame[fres,] ## accessing the spillover matrix try(spillover(frame)) ## check equality frame2 <- frame frame == frame2 exprs(frame2) <- exprs(frame)*2 frame == frame2 } \keyword{classes}