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Add coercion method from ExpressionSets; DataLayer docs
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‎DESCRIPTION

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Package: SingleCellAssay
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Type: Package
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Title: Core data structures for single-cell assays
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Version: 0.79
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Version: 0.80
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Date: 2014-04-08
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Author: Andrew McDavid <[email protected]>, Greg Finak <[email protected]>
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Maintainer: Greg Finak <[email protected]>

‎R/AllClasses.R

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NULL
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#setOldClass("ncdf")
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##' DataLayer class
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##'
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##' DataLayer is a 3-D array, wrapped to make it look like a matrix.
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##' It is used to hold matrix-like expression data, for which we might want to keep several representations (transformations) around.
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##' The number of matrix "layers" is given by the trailing dimension.
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##' Dimensions 1 and 2 correspond to the "rows" and "columns" of the matrix.
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##' The layer that is active can be set, and additional layers created (concatenated).
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##' }
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##' \section{Slots}{
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##' DataLayer extends array, and has the following additional slots
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##' \describe{
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##' \item{.Data}{the underlying array}
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##' \item{valid}{a \code{logical} that may optionally indicate the freshness of derived layers (if the underlying data changes). Not currently used.}
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##' \item{layer}{which 'slice' of the array is being used}
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##' }}
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##' \section{Methods}{
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##' \describe{
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##' \item{addlayer}{Concatentate another slice onto the object}
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##' \item{layername}{Return the name of the current slice}
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##' \item{layer}{Return the active layer}
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##' \item{layer<-}{Set the active layer}
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##' \item{exprs}{Return the matrix representation of the active layer}
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##' \item{exprs<-}{Replace the matrix on the current layer.}
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##' }
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##' @examples
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##' ar <- array(1:10, dim=c(2, 5, 1))
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##' dl <- new('DataLayer', .Data=ar)
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##' nrow(dl) #2
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##' ncol(dl) #5
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##' layer(dl)
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##' dl <- addlayer(dl, 'negative')
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##' ex <- exprs(dl)
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##' layer(dl) <- 'negative' #or could use 2
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##' exprs(dl)<- -ex
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##' exprs(dl)
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##' @name DataLayer-class
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##' @docType class
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##' @aliases DataLayer
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##' @seealso \code{\link{SingleCellAssay}}, \code{\link{SingleCellAssay-class}}
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setClass('DataLayer', contains='array', representation=representation(layer='numeric', valid='logical'), prototype=prototype(array(NA, dim=c(0, 0, 1)), layer=1L, valid=TRUE), validity=function(object){
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#cat('DL dim ', dim([email protected]), '\n')
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length(dim(object@.Data))==3

‎R/DataLayer.R

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@@ -115,7 +115,11 @@ setMethod("exprs",signature(object="DataLayer"),function(object){
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setMethod('initialize', 'DataLayer',
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function(.Object, ...){
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## message('init DataLayer') #DEBUG
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## This is (was?) necessary initialize since we inherit from 'array'
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## But is rather mysterious, nonetheless.
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.Object <- getMethod('initialize', 'ANY')(.Object, ...)
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dn <- dimnames(.Object@.Data)
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dimnames(.Object@.Data) <-if(is.null(dn)) list(wells=NULL, features=NULL, layers=NULL) else dn
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.Object
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})
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‎R/Fluidigm-methods.R

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@@ -237,7 +237,7 @@ filter <- function(sc, groups=NULL, filt_control=NULL, apply_filter=TRUE){
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if (!is.null(groups)) {
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checkGroups(sc, groups)
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scL <- split(sc, groups)
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lapp <- lapply(scL, filter, groups=NULL, filt_control, apply_filter)
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lapp <- lapply(scL, filter, groups=NULL, filt_control=filt_control, apply_filter=apply_filter)
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## Do various things with lapp:
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if(apply_filter && filt_control$filter){
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## list of SingleCellAssays

‎R/SingleCellAssay-methods.R

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@@ -204,7 +204,7 @@ fixdf <- function(df, idvars, primerid, measurement, cmap, fmap, keep.names){
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## unnamed arguments get passed along to callNextMethod
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## which eventually just sets the slots
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setMethod('initialize', 'SingleCellAssay',
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function(.Object, dataframe, idvars, primerid, measurement, cellvars=NULL, featurevars=NULL, phenovars=NULL, sort=TRUE, ...){
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function(.Object, dataframe, idvars, primerid, measurement, exprsMatrix, cellvars=NULL, featurevars=NULL, phenovars=NULL, sort=TRUE, ...){
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##message(class(.Object), ' calling SingleCellAssay Initialize') #DEBUG
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.Object <- callNextMethod()
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if(sort) .Object <- sort(.Object)
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slot(x, along) <- newdata
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x
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})
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setAs('ExpressionSet', 'SingleCellAssay', function(from){
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## just a transposed version
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ex <- t(exprs(from))
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dn <- dimnames(ex)
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names(dn) <- c('wellKey', 'primerid')
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dim(ex) <- c(dim(ex), 1)
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pd <- phenoData(from)
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pData(pd)[,'wellKey'] <- sampleNames(pd)
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fd <- featureData(from)
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fd$primerid <- sampleNames(fd)
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dimnames(ex) <- c(dn, layer='ExpressionSet')
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DL <- new('DataLayer', .Data=ex)
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new('SingleCellAssay', .Data=DL, featureData=fd, cellData=pd, sort=FALSE)
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})
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## setAs('SingleCellAssay', 'data.table', function(from){
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## dt <- data.table(as.vector(exprs(from)))
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## })

‎inst/tests/test-DataLayer.R

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@@ -36,19 +36,19 @@ test_that('doubleton dl works', {
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context('subset and replace')
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test_that('subset works', {
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expect_equal(dl[[,1]], mat[,1,drop=FALSE])
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expect_equal(dl[[1,]], mat[1,,drop=FALSE])
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expect_equal(dl[[,1]], mat[,1,drop=FALSE], check.names=FALSE)
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expect_equal(dl[[1,]], mat[1,,drop=FALSE], check.names=FALSE)
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matidx <- cbind(c(1, 1, 2), 1:3)
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expect_equal(dl[[matidx]], mat[matidx])
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mat[matidx] <- -999
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dl[[matidx]] <- -999
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expect_equal(exprs(dl), mat)
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expect_equal(exprs(dl), mat, check.attributes=FALSE)
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})
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test_that('[ subscripting works', {
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expect_is(dl[1,], 'DataLayer')
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expect_is(dl[,2:3], 'DataLayer')
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expect_equal(exprs(dl[1,]), dl[[1,,drop=FALSE]])
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expect_equal(exprs(dl[1,]), dl[[1,,drop=FALSE]], check.attributes=FALSE)
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})
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spl <- split(dl, 1:2)

‎man/DataLayer-class.Rd

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\docType{class}
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\name{DataLayer-class}
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\alias{DataLayer}
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\alias{DataLayer-class}
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\title{DataLayer class}
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\description{
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DataLayer is a 3-D array, wrapped to make it look like a
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matrix. It is used to hold matrix-like expression data, for
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which we might want to keep several representations
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(transformations) around. The number of matrix "layers" is
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given by the trailing dimension. Dimensions 1 and 2
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correspond to the "rows" and "columns" of the matrix. The
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layer that is active can be set, and additional layers
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created (concatenated). } \section{Slots}{ DataLayer
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extends array, and has the following additional slots
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\describe{ \item{.Data}{the underlying array}
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\item{valid}{a \code{logical} that may optionally indicate
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the freshness of derived layers (if the underlying data
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changes). Not currently used.} \item{layer}{which 'slice'
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of the array is being used} }} \section{Methods}{
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\describe{ \item{addlayer}{Concatentate another slice onto
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the object} \item{layername}{Return the name of the current
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slice} \item{layer}{Return the active layer}
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\item{layer<-}{Set the active layer} \item{exprs}{Return
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the matrix representation of the active layer}
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\item{exprs<-}{Replace the matrix on the current layer.} }
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}
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\examples{
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ar <- array(1:10, dim=c(2, 5, 1))
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dl <- new('DataLayer', .Data=ar)
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nrow(dl) #2
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ncol(dl) #5
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layer(dl)
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dl <- addlayer(dl, 'negative')
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ex <- exprs(dl)
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layer(dl) <- 'negative' #or could use 2
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exprs(dl)<- -ex
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exprs(dl)
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}
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\seealso{
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\code{\link{SingleCellAssay}},
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\code{\link{SingleCellAssay-class}}
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}
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