Add coercion method from ExpressionSets; DataLayer docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SingleCellAssay
 Type: Package
 Title: Core data structures for single-cell assays
-Version: 0.79
+Version: 0.80
 Date: 2014-04-08
 Author: Andrew McDavid <amcdavid@fhcrc.org>, Greg Finak <gfinak@fhcrc.org>
 Maintainer: Greg Finak <gfinak@fhcrc.org>

R/AllClasses.R

@@ -5,8 +5,46 @@
 
 NULL
 
-#setOldClass("ncdf")
 
+##' DataLayer class
+##' 
+##' DataLayer is a 3-D array, wrapped to make it look like a matrix.
+##' It is used to hold matrix-like expression data, for which we might want to keep several representations (transformations) around.
+##' The number of matrix "layers" is given by the trailing dimension.
+##' Dimensions 1 and 2 correspond to the "rows" and "columns" of the matrix.
+##' The layer that is active can be set, and additional layers created (concatenated).
+##' }
+##' \section{Slots}{
+##' DataLayer extends array, and has the following additional slots
+##' \describe{
+##'   \item{.Data}{the underlying array}
+##'   \item{valid}{a \code{logical} that may optionally indicate the freshness of derived layers (if the underlying data changes).  Not currently used.}
+##'   \item{layer}{which 'slice' of the array is being used}
+##' }}
+##' \section{Methods}{
+##' \describe{
+##' \item{addlayer}{Concatentate another slice onto the object}
+##' \item{layername}{Return the name of the current slice}
+##' \item{layer}{Return the active layer}
+##' \item{layer<-}{Set the active layer}
+##' \item{exprs}{Return the matrix representation of the active layer}
+##' \item{exprs<-}{Replace the matrix on the current layer.}
+##' }
+##' @examples
+##' ar <- array(1:10, dim=c(2, 5, 1))
+##' dl <- new('DataLayer', .Data=ar)
+##' nrow(dl) #2
+##' ncol(dl) #5
+##' layer(dl)
+##' dl <- addlayer(dl, 'negative')
+##' ex <- exprs(dl)
+##' layer(dl) <- 'negative' #or could use 2
+##' exprs(dl)<- -ex
+##' exprs(dl)
+##' @name DataLayer-class
+##' @docType class 
+##' @aliases DataLayer
+##' @seealso \code{\link{SingleCellAssay}}, \code{\link{SingleCellAssay-class}}
 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){
   #cat('DL dim ', dim(object@.Data), '\n')
   length(dim(object@.Data))==3

R/DataLayer.R

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

R/Fluidigm-methods.R

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

R/SingleCellAssay-methods.R

@@ -204,7 +204,7 @@ fixdf <- function(df, idvars, primerid, measurement, cmap, fmap, keep.names){
 ## unnamed arguments get passed along to callNextMethod
 ## which eventually just sets the slots
 setMethod('initialize', 'SingleCellAssay',
-          function(.Object, dataframe, idvars, primerid, measurement, cellvars=NULL, featurevars=NULL, phenovars=NULL, sort=TRUE, ...){
+          function(.Object, dataframe, idvars, primerid, measurement, exprsMatrix, cellvars=NULL, featurevars=NULL, phenovars=NULL, sort=TRUE, ...){
             ##message(class(.Object), ' calling SingleCellAssay Initialize')  #DEBUG
             .Object <- callNextMethod()
             if(sort) .Object <- sort(.Object)
@@ -639,3 +639,23 @@ setMethod('combine', signature=c(x='SingleCellAssay', y='AnnotatedDataFrame'), f
   slot(x, along) <- newdata
   x
 })
+
+setAs('ExpressionSet', 'SingleCellAssay', function(from){
+    ## just a transposed version
+    ex <- t(exprs(from))
+    dn <- dimnames(ex)
+    names(dn) <- c('wellKey', 'primerid')
+    dim(ex) <- c(dim(ex), 1)
+    pd <- phenoData(from)
+    pData(pd)[,'wellKey'] <- sampleNames(pd)
+    fd <- featureData(from)
+    fd$primerid <- sampleNames(fd)
+    dimnames(ex) <- c(dn, layer='ExpressionSet')
+    DL <- new('DataLayer', .Data=ex)
+    new('SingleCellAssay', .Data=DL, featureData=fd, cellData=pd, sort=FALSE)
+})
+
+## setAs('SingleCellAssay', 'data.table', function(from){
+## dt <- data.table(as.vector(exprs(from)))
+
+## })

inst/tests/test-DataLayer.R

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

man/DataLayer-class.Rd

@@ -0,0 +1,44 @@
+\docType{class}
+\name{DataLayer-class}
+\alias{DataLayer}
+\alias{DataLayer-class}
+\title{DataLayer class}
+\description{
+DataLayer is a 3-D array, wrapped to make it look like a
+matrix. It is used to hold matrix-like expression data, for
+which we might want to keep several representations
+(transformations) around. The number of matrix "layers" is
+given by the trailing dimension. Dimensions 1 and 2
+correspond to the "rows" and "columns" of the matrix. The
+layer that is active can be set, and additional layers
+created (concatenated). } \section{Slots}{ DataLayer
+extends array, and has the following additional slots
+\describe{ \item{.Data}{the underlying array}
+\item{valid}{a \code{logical} that may optionally indicate
+the freshness of derived layers (if the underlying data
+changes).  Not currently used.} \item{layer}{which 'slice'
+of the array is being used} }} \section{Methods}{
+\describe{ \item{addlayer}{Concatentate another slice onto
+the object} \item{layername}{Return the name of the current
+slice} \item{layer}{Return the active layer}
+\item{layer<-}{Set the active layer} \item{exprs}{Return
+the matrix representation of the active layer}
+\item{exprs<-}{Replace the matrix on the current layer.} }
+}
+\examples{
+ar <- array(1:10, dim=c(2, 5, 1))
+dl <- new('DataLayer', .Data=ar)
+nrow(dl) #2
+ncol(dl) #5
+layer(dl)
+dl <- addlayer(dl, 'negative')
+ex <- exprs(dl)
+layer(dl) <- 'negative' #or could use 2
+exprs(dl)<- -ex
+exprs(dl)
+}
+\seealso{
+\code{\link{SingleCellAssay}},
+\code{\link{SingleCellAssay-class}}
+}
+