Remove all spatialData-related documentation, code & comments

NAMESPACE

@@ -8,8 +8,6 @@ export("imgSource<-")
 export("molecules<-")
 export("spatialCoords<-")
 export("spatialCoordsNames<-")
-export("spatialData<-")
-export("spatialDataNames<-")
 export(SpatialExperiment)
 export(SpatialImage)
 export(addImg)
@@ -30,8 +28,6 @@ export(rotateObject)
 export(scaleFactors)
 export(spatialCoords)
 export(spatialCoordsNames)
-export(spatialData)
-export(spatialDataNames)
 export(toSpatialExperiment)
 exportClasses(LoadedSpatialImage)
 exportClasses(RemoteSpatialImage)
@@ -47,8 +43,6 @@ exportMethods("imgSource<-")
 exportMethods("molecules<-")
 exportMethods("spatialCoords<-")
 exportMethods("spatialCoordsNames<-")
-exportMethods("spatialData<-")
-exportMethods("spatialDataNames<-")
 exportMethods(addImg)
 exportMethods(dim)
 exportMethods(getImg)
@@ -66,16 +60,12 @@ exportMethods(rotateObject)
 exportMethods(scaleFactors)
 exportMethods(spatialCoords)
 exportMethods(spatialCoordsNames)
-exportMethods(spatialData)
-exportMethods(spatialDataNames)
 importClassesFrom(S4Vectors,Annotated)
 importFrom(BiocGenerics,cbind)
 importFrom(BiocGenerics,rbind)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,isEmpty)
-importFrom(S4Vectors,make_zero_col_DFrame)
-importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,setValidity2)
 importFrom(SingleCellExperiment,"int_colData<-")
 importFrom(SingleCellExperiment,"int_metadata<-")

R/AllGenerics.R

@@ -35,18 +35,6 @@ setGeneric("mirrorImg", function(x, ...) standardGeneric("mirrorImg"))
 
 # SpatialExperiment methods ----------------------------------------------------
 
-#' @export
-setGeneric("spatialData", function(x, ...) standardGeneric("spatialData"))
-
-#' @export
-setGeneric("spatialData<-", function(x, value) standardGeneric("spatialData<-"))
-
-#' @export
-setGeneric("spatialDataNames", function(x) standardGeneric("spatialDataNames"))
-
-#' @export
-setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialDataNames<-"))
-
 #' @export
 setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))
 

R/SpatialExperiment-colData.R

@@ -99,7 +99,6 @@ setReplaceMethod("colData",
 setReplaceMethod("colData",
     c("SpatialExperiment", "NULL"),
     function(x, value) {
-        spatialDataNames(x) <- NULL
         value <- colData(x)["sample_id"]
         colData(x) <- value
         return(x)

R/SpatialExperiment-methods.R

@@ -3,8 +3,6 @@
 #' @title Methods for spatial attributes
 #' 
 #' @aliases
-#' spatialData spatialData<-
-#' spatialDataNames spatialDataNames<-
 #' spatialCoords spatialCoords<-
 #' spatialCoordsNames spatialCoordsNames<-
 #' imgData imgData<-
@@ -28,39 +26,21 @@
 #' @details
 #' Additional details for each type of data attribute are provided below.
 #' 
-#' Note: \code{\link{spatialData}} and \code{\link{spatialDataNames}}
-#' (previously used to store a subset of columns from \code{\link{colData}})
-#' have been deprecated. All columns should be stored in either
-#' \code{\link{spatialCoords}} (numeric matrix containing spatial coordinates)
-#' or \code{\link{colData}} (all other columns). The
-#' \code{spatialData}/\code{spatialDataNames} functionality has been retained
-#' for backward compatibility but may be removed in the future.
-#' 
 #' See \code{\link{rotateCoords}}, \code{\link{mirrorCoords}},
 #' \code{\link{rotateObject}}, or \code{\link{mirrorObject}} for details on
 #' methods to rotate and mirror SpatialExperiment objects and their
 #' \code{spatialCoords}.
 #' 
-#' @section spatialData and spatialCoords methods:
+#' @section spatialCoords methods:
 #' \describe{
-#' \item{\code{spatialData(x) <- value}: }{
-#'   The \code{spatialData} setter expects a \code{DataFrame}. 
-#'   If the input does not contain an \code{in_tissue} column, 
-#'   this will be included with a default value of \code{1}.}
 #' \item{\code{spatialCoords(x)}: }{
 #'   Getter for numeric matrix of spatial coordinates.}
 #' \item{\code{spatialCoords(x) <- value}: }{
 #'   Setter for numeric matrix of spatial coordinates.}
 #' }
 #' 
-#' @section spatialDataNames and spatialCoordsNames methods:
+#' @section spatialCoordsNames methods:
 #' \describe{
-#' \item{\code{spatialDataNames(x)}: }{
-#'   Returns the names of the \code{colData} associated with the 
-#'   spatial information, which are stored in the \code{int_metadata}.}
-#' \item{\code{spatialDataNames(x) <- value}: }{
-#'   Setter to replace column names
-#'   in the \code{spatialData} \code{DataFrame}.}
 #' \item{\code{spatialCoordsNames(x)}: }{
 #'   Returns the defined names of the
 #'   spatial coordinates (e.g. \code{c("x", "y")}).}
@@ -110,86 +90,6 @@
 #'   sample_id = cd$sample_id)
 NULL
 
-# spatialData ------------------------------------------------------------------
-
-#' @rdname SpatialExperiment-methods
-#' @importFrom SummarizedExperiment colData
-#' @export
-setMethod("spatialData", 
-    "SpatialExperiment",
-    function(x) {
-        colData(x)[spatialDataNames(x)]
-    }
-)
-
-#' @rdname SpatialExperiment-methods
-#' @importFrom SummarizedExperiment colData colData<-
-#' @export
-setReplaceMethod("spatialData", 
-    c("SpatialExperiment", "DFrame"),
-    function(x, value) {
-        stopifnot(nrow(value) == ncol(x))
-        out <- colData(x)
-        old <- names(out)
-        new <- names(value)
-        dup <- intersect(old, new)
-        if (length(dup) > 0) {
-            out[dup] <- value
-            value <- value[setdiff(new, dup)]
-        }
-        out <- cbind(out, value)
-        colData(x) <- out
-        spatialDataNames(x) <- new
-        return(x)
-    }
-)
-
-#' @rdname SpatialExperiment-methods
-#' @importFrom S4Vectors make_zero_col_DFrame
-#' @export
-setReplaceMethod("spatialData", 
-    c("SpatialExperiment", "NULL"),
-    function(x, value) {
-        `spatialDataNames<-`(x, value)
-    }
-)
-
-# spatialDataNames -------------------------------------------------------------
-
-#' @rdname SpatialExperiment-methods
-#' @importFrom S4Vectors metadata
-#' @export
-setMethod("spatialDataNames", 
-    "SpatialExperiment", 
-    function(x) {
-        .msg_spatialData()
-        int_metadata(x)$spatialDataNames
-    }
-)
-
-#' @rdname SpatialExperiment-methods
-#' @importFrom SummarizedExperiment colData
-#' @importFrom SingleCellExperiment int_metadata<-
-#' @export
-setReplaceMethod("spatialDataNames", 
-    c("SpatialExperiment", "character"),
-    function(x, value) {
-        stopifnot(value %in% names(colData(x)))
-        int_metadata(x)$spatialDataNames <- value
-        return(x)
-    }
-)
-
-#' @rdname SpatialExperiment-methods
-#' @export
-setReplaceMethod("spatialDataNames",
-    c("SpatialExperiment", "NULL"),
-    function(x, value) {
-        value <- character()
-        `spatialDataNames<-`(x, value)
-    }
-)
-
 # spatialCoords ----------------------------------------------------------------
 
 #' @rdname SpatialExperiment-methods
@@ -268,13 +168,6 @@ setMethod("scaleFactors",
 
 # utils ------------------------------------------------------------------------
 
-# message for deprecation of spatialData/Names
-.msg_spatialData <- function() {
-    message(paste0(
-        "Note: spatialData and spatialDataNames have been deprecated; all ", 
-        "columns should be stored in colData and spatialCoords"))
-}
-
 #' @export
 #' @importFrom utils .DollarNames
 .DollarNames.SpatialExperiment <- function(x, pattern = "")

R/SpatialExperiment.R

@@ -44,22 +44,6 @@
 #'   \code{imageSources}) containing unique image identifiers.
 #' @param loadImage Logical indicating whether to load image into memory.
 #'   Default = \code{FALSE}.
-#' @param spatialDataNames (Deprecated) A \code{character} vector of column
-#'   names from \code{\link{colData}} to include in \code{\link{spatialData}}.
-#'   Alternatively, the \code{spatialData} argument may be provided. If both are
-#'   provided, \code{spatialDataNames} is given precedence, and a warning is
-#'   returned. (Note: \code{spatialData} and \code{spatialDataNames} have been
-#'   deprecated; \code{colData} and \code{spatialCoords} should be used for all
-#'   columns. The arguments have been retained for backward compatibility but
-#'   may be removed in the future.)
-#' @param spatialData (Deprecated) A \code{\link{DataFrame}} containing columns
-#'   to store in \code{\link{spatialData}}, which must contain at least the
-#'   columns of spatial coordinates. Alternatively, \code{spatialDataNames} may
-#'   be provided. If both are provided, \code{spatialDataNames} is given
-#'   precedence, and a warning is returned. (Note: \code{spatialData} and
-#'   \code{spatialDataNames} have been deprecated; \code{colData} and
-#'   \code{spatialCoords} should be used for all columns. The arguments have
-#'   been retained for backward compatibility but may be removed in the future.)
 #' 
 #' @details
 #' In this class, rows represent genes, and columns represent spots (for
@@ -217,9 +201,7 @@ SpatialExperiment <- function(...,
     imageSources=NULL,
     image_id=NULL,
     loadImage=FALSE,
-    imgData=NULL,
-    spatialDataNames=NULL,
-    spatialData=NULL) {
+    imgData=NULL) {
 
     sce <- SingleCellExperiment(...)
     spe <- .sce_to_spe(sce=sce, 
@@ -230,9 +212,7 @@ SpatialExperiment <- function(...,
         imageSources=imageSources,
         image_id=image_id,
         loadImage=loadImage,
-        imgData=imgData,
-        spatialDataNames=spatialDataNames,
-        spatialData=spatialData)
+        imgData=imgData)
     return(spe)
 }
 
@@ -247,9 +227,7 @@ SpatialExperiment <- function(...,
     imageSources=NULL,
     image_id=NULL,
     loadImage=TRUE,
-    imgData=NULL,
-    spatialDataNames=NULL,
-    spatialData=NULL) {
+    imgData=NULL) {
 
     old <- S4Vectors:::disableValidity()
     if (!isTRUE(old)) {
@@ -270,40 +248,29 @@ SpatialExperiment <- function(...,
         sample_id <- unique(sce$sample_id)
     }
 
-    if (!is.null(spatialData) || !is.null(spatialDataNames)) {
-      .msg_spatialData()
-    }
-
     spe <- new("SpatialExperiment", sce)
 
     # in the following code chunk, we give precedence 
-    # to spatialData/CoordsNames over spatialData/Coords
-    #   where spatialDataNames should be in colData,
-    #   and spatialCoordsNames can be in both colData and spatialData
-    # if both spatialData/Coords and -Names are supplied
+    # to spatialCoordsNames over spatialCoords
+    #   where spatialCoordsNames should be in colData
+    # if both spatialCoords and -Names are supplied
     #   we give an informative warning notifying the user
-    #   that spatialData/CoordsNames will be used 
+    #   that spatialCoordsNames will be used 
 
     msg <- function(.) message(sprintf(                
         "Both '%s' and '%sNames'  have been supplied;\nusing '%s'. ", ., ., .),
         "Set either to NULL to suppress this message.")
 
     if (!is.null(spatialCoordsNames)) {
         stopifnot(is.character(spatialCoordsNames),
-            all(spatialCoordsNames %in% names(colData(spe)))
-            || all(spatialCoordsNames %in% names(spatialData)))
+            all(spatialCoordsNames %in% names(colData(spe))))
         if (!is.null(spatialCoords))
             msg("spatialCoords")
         if (all(spatialCoordsNames %in% names(colData(spe)))) {
             i <- spatialCoordsNames
             j <- setdiff(names(colData(spe)), i)
             spatialCoords(spe) <- as.matrix(colData(spe)[i])
             colData(spe) <- colData(spe)[j]
-        } else {
-            i <- spatialCoordsNames
-            j <- setdiff(names(spatialData), i)
-            spatialCoords(spe) <- as.matrix(spatialData[i])
-            spatialData <- spatialData[j]
         }
     } else if (!is.null(spatialCoords)) {
         stopifnot(
@@ -315,26 +282,6 @@ SpatialExperiment <- function(...,
         spatialCoords(spe) <- NULL
     }
 
-    if (!is.null(spatialDataNames)) {
-        stopifnot(
-            is.character(spatialDataNames), 
-            spatialDataNames %in% names(colData(spe)))
-        if (!is.null(spatialData)) 
-            msg("spatialData")
-        i <- spatialDataNames
-        j <- setdiff(names(colData(spe)), i)
-        spd <- colData(spe)[i]
-        colData(spe) <- colData(spe)[j]
-        spatialData(spe) <- spd
-    } else if (!is.null(spatialData)) {
-        stopifnot(
-            is(spatialData, "DFrame"),
-            nrow(spatialData) == ncol(spe))
-        spatialData(spe) <- spatialData
-    } else {
-        spatialData(spe) <- NULL
-    }
-
     if (!is.null(imgData)) {
         stopifnot(imgData$sample_id %in% spe$sample_id)
         imgData(spe) <- imgData

R/Validity.R

@@ -13,16 +13,6 @@
     return(msg)
 }
 
-.spatialData_validity <- function(x, msg=NULL) {
-    y <- colData(x)[int_metadata(x)$spatialDataNames]
-    if (!is.null(y) && !is(y, "DFrame")) {
-        msg <- c(msg, paste(
-            "'spatialData' field in 'int_colData'",
-            "should be a 'DFrame'"))
-    }
-    return(msg)
-}
-
 .colData_validity <- function(obj, msg=NULL) {
     df <- colData(obj)
     if (is.null(df$sample_id)) { 
@@ -86,9 +76,7 @@
     msg <- NULL
     msg <- .colData_validity(object, msg)
     msg <- .imgData_validity(object, msg)
-    msg <- .spatialData_validity(object, msg)
     msg <- .spatialCoords_validity(object, msg)
-    #msg <- .spatialDataNames_validity(object, msg)
     if (length(msg)) return(msg)
     return(TRUE)
 }