R/addPlottingFactor.R
In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data
#' Add plotting factor to \code{\link{SpatialOverlay}} object
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots object with annotation: can be \code{NanoStringGeoMxSet},
#' \code{data.frame}, \code{matrix}, or vector containing
#' \code{character}, \code{factor}, or \code{numeric}
#' @param plottingFactor column or row from annots to add as plotting factor,
#' if using vector this will be the name of the new
#' plotting factor
#' @param ... if using \code{NanoStringGeoMxSet}, name of count matrix to pull
#' counts from
#'
#' @return \code{\link{SpatialOverlay}} object with new plotting factor
#'
#' @examples
#' muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
#' package = "SpatialOmicsOverlay")))
#'
#' muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt",
#' package = "SpatialOmicsOverlay")
#'
#' muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = muBrainLW,
#' plottingFactor = "segment")
#'
#' muBrainGxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip",
#' package = "SpatialOmicsOverlay")))
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = muBrainGxT,
#' plottingFactor = "Calm1",
#' countMatrix = "exprs")
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = seq_len(length(sampNames(muBrain))),
#' plottingFactor = "ROINum")
#'
#' head(plotFactors(muBrain))
#'
#' @export
#'
setGeneric("addPlottingFactor", signature = "annots",
function(overlay, annots, plottingFactor, ...)
standardGeneric("addPlottingFactor"))
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{NanoStringGeoMxSet} object
#' @param plottingFactor column or row from annots to add as plotting factor
#' @param countMatrix name of count matrix to pull counts from
#'
#' @export
#' @rdname addPlottingFactor
#'
#' @importFrom Biobase assayDataElement
#'
setMethod("addPlottingFactor", "NanoStringGeoMxSet",
function(overlay, annots, plottingFactor, countMatrix = "exprs"){
if(!is(overlay,"SpatialOverlay")){
stop("overlay must be a SpatialOverlay object")
}
if(length(plottingFactor) > 1){
warning("Plotting factors must be added 1 at a time, continuing with only the first factor")
plottingFactor <- plottingFactor[1]
}
if(is.null(plottingFactor)){
stop("Please provide valid plottingFactor")
}
if(!plottingFactor %in% colnames(sData(annots)) &
!plottingFactor %in% rownames(annots)){
stop("plottingFactor was not in given annots")
}
if(plottingFactor %in% colnames(sData(annots))){
axis <- "col"
}else{
axis <- "row"
}
samples <- sampNames(overlay)
gxtSamples <- gsub(".dcc", "", rownames(sData(annots)))
if(any(!samples %in% gxtSamples)){
sampIDs <- which(apply(as.matrix(sData(annots)), 2,
function(x){any(samples %in% x)}))
if(length(sampIDs) == 0){
stop("Sample IDs in SpatialOverlay do not match given annots")
}else if(length(sampIDs) > 1){
matchingSamps <- NULL
for(i in names(sampIDs)){
matchingSamps[i] <- length(sData(annots)[[i]] %in% samples)
}
sampIDs <- names(sort(matchingSamps, decreasing = TRUE)[1L])
}
gxtSamples <- sData(annots)[[sampIDs]]
}
annots <- annots[,match(samples, gxtSamples, nomatch = 0)]
gxtSamples <- gsub(".dcc", "", rownames(sData(annots)))
samples <- samples[match(gxtSamples, samples, nomatch = 0)]
if(length(samples) != length(sampNames(overlay))){
warning(paste("Missing annotations in annots. Samples missing:",
paste(sampNames(overlay)[!sampNames(overlay) %in%
samples],
collapse = ", ")))
overlay <- removeSample(overlay = overlay,
remove = sampNames(overlay)[which(!sampNames(overlay) %in%
samples)])
}
if(plottingFactor %in% colnames(plotFactors(overlay))){
if(axis == "col"){
overlay@plottingFactors[[plottingFactor]] <- sData(annots)[[plottingFactor]]
}else{
overlay@plottingFactors[[plottingFactor]] <- Biobase::assayDataElement(annots,
elt = countMatrix)[rownames(annots) ==
plottingFactor,]
}
}else{
if(axis == "col"){
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
sData(annots)[[plottingFactor]]))
}else{
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
Biobase::assayDataElement(annots,
elt = countMatrix)[rownames(annots) ==
plottingFactor,]))
}
rownames(overlay@plottingFactors) <- samples
colnames(overlay@plottingFactors)[ncol(plotFactors(overlay))] <- plottingFactor
}
if(is(plotFactors(overlay)[,ncol(plotFactors(overlay))], "character")){
overlay@plottingFactors[,ncol(plotFactors(overlay))] <- as.factor(plotFactors(overlay)[,ncol(plotFactors(overlay))])
}
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{matrix} containing plottingFactor, column or column names
#' must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "matrix",
function(overlay, annots, plottingFactor){
return(addPlottingFactor(annots = as.data.frame(annots),
overlay = overlay,
plottingFactor = plottingFactor))
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{matrix} containing plottingFactor, column or column names
#' must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "tbl_df",
function(overlay, annots, plottingFactor){
return(addPlottingFactor(annots = as.data.frame(annots),
overlay = overlay,
plottingFactor = plottingFactor))
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{matrix} containing plottingFactor, column or column names
#' must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "tbl",
function(overlay, annots, plottingFactor){
return(addPlottingFactor(annots = as.data.frame(annots),
overlay = overlay,
plottingFactor = plottingFactor))
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{data.frame} containing plottingFactor, column or column
#' names must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "data.frame",
function(overlay, annots, plottingFactor){
if(!is(overlay,"SpatialOverlay")){
stop("overlay must be a SpatialOverlay object")
}
if(length(plottingFactor) > 1){
warning("Plotting factors must be added 1 at a time, continuing with only the first factor")
plottingFactor <- plottingFactor[1]
}
if(is.null(plottingFactor)){
stop("Please provide valid plottingFactor")
}
if(!plottingFactor %in% colnames(annots) &
!plottingFactor %in% rownames(annots)){
stop("plottingFactor was not in given annots")
}
if(plottingFactor %in% colnames(annots)){
axis <- "col"
}else if(plottingFactor %in% rownames(annots)){
axis <- "row"
}else{
stop("plottingFactor must be in row or column names of annots")
}
samples <- sampNames(overlay)
if(axis == "col"){
sampIDs <- which(apply(annots, 2, function(x){any(samples %in%
x)}))
if(length(sampIDs) == 0){
stop("Sample IDs in SpatialOverlay do not match given annots")
}else if(length(sampIDs) > 1){
matchingSamps <- NULL
for(i in names(sampIDs)){
matchingSamps[i] <- length(annots[[i]] %in% samples)
}
sampIDs <- names(sort(matchingSamps, decreasing = TRUE)[1L])
}
annots <- annots[match(samples, annots[,sampIDs],
nomatch = 0),]
samples <- samples[match(annots[,sampIDs], samples,
nomatch = 0)]
}else{
annots <- annots[,match(samples, colnames(annots),
nomatch = 0)]
samples <- samples[match(colnames(annots), samples,
nomatch = 0)]
}
if(length(samples) != length(sampNames(overlay))){
warning(paste("Missing annotations in annots. Samples missing:",
paste(sampNames(overlay)[!sampNames(overlay) %in%
samples],
collapse = ", ")))
overlay <- removeSample(overlay = overlay,
remove = sampNames(overlay)[which(!sampNames(overlay) %in%
samples)])
}
if(plottingFactor %in% colnames(plotFactors(overlay))){
if(axis == "col"){
overlay@plottingFactors[[plottingFactor]] <- annots[[plottingFactor]]
}else{
overlay@plottingFactors[[plottingFactor]] <- t(annots[rownames(annots) ==
plottingFactor,])
}
}else{
if(axis == "col"){
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
annots[[plottingFactor]]))
}else{
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
t(annots[rownames(annots) ==
plottingFactor,])))
}
rownames(overlay@plottingFactors) <- samples
colnames(overlay@plottingFactors)[ncol(plotFactors(overlay))] <- plottingFactor
}
if(is(plotFactors(overlay)[,ncol(plotFactors(overlay))],"character")){
overlay@plottingFactors[,ncol(plotFactors(overlay))] <- as.factor(plotFactors(overlay)[,ncol(plotFactors(overlay))])
}
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots character vector with the plottingFactor. if names match sample
#' names in overlay vector will be matched on those,
#' otherwise assumed in the correct order
#' @param plottingFactor name of the new plotting factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "character",
function(overlay, annots, plottingFactor){
if(!is(overlay,"SpatialOverlay")){
stop("overlay must be a SpatialOverlay object")
}
if(is.null(plottingFactor)){
stop("Please provide valid plottingFactor")
}
if(is.null(names(annots))){
warning("No names on vector, assuming data is in same order as overlay",
immediate. = TRUE)
}
samples <- names(annots)
if(length(annots) < length(sampNames(overlay))){
if(is.null(names(annots))){
stop("Length of annots does not match samples in overlay & there are no names to match to")
}
warning(paste("Missing annotations in annots. Samples missing:",
paste(sampNames(overlay)[!sampNames(overlay) %in%
samples],
collapse = ", ")))
overlay <- removeSample(overlay = overlay,
remove = sampNames(overlay)[which(!sampNames(overlay) %in%
samples)])
}
samples <- sampNames(overlay)
if(plottingFactor %in% colnames(plotFactors(overlay))){
if(is.null(names(annots))){
annots <- annots[seq_len(length(samples))]
}else{
annots <- annots[match(samples, names(annots), nomatch = 0)]
samples <- samples[match(names(annots), samples, nomatch = 0)]
}
overlay@plottingFactors[[plottingFactor]] <- annots
}else{
if(!is.null(samples)){
if(is.null(names(annots))){
annots <- annots[seq_len(length(samples))]
}else{
annots <- annots[match(samples, names(annots), nomatch = 0)]
samples <- samples[match(names(annots), samples, nomatch = 0)]
}
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
annots))
}else{
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
t(annots)))
}
rownames(overlay@plottingFactors) <- samples
colnames(overlay@plottingFactors)[ncol(plotFactors(overlay))] <- plottingFactor
}
if(is(plotFactors(overlay)[,ncol(plotFactors(overlay))],"character")){
overlay@plottingFactors[,ncol(plotFactors(overlay))] <-
as.factor(plotFactors(overlay)[,ncol(plotFactors(overlay))])
}
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots numeric vector with the plottingFactor. if names match sample
#' names in overlay vector will be matched on those,
#' otherwise assumed in the correct order
#' @param plottingFactor name of the new plotting factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "numeric",
function(overlay, annots, plottingFactor){
overlay <- addPlottingFactor(overlay,
setNames(as.character(annots),
names(annots)),
plottingFactor)
overlay@plottingFactors[,ncol(plotFactors(overlay))] <- as.numeric(as.character(plotFactors(overlay)[,ncol(plotFactors(overlay))]))
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots factor vector with the plottingFactor. if names match sample
#' names in overlay vector will be matched on those,
#' otherwise assumed in the correct order
#' @param plottingFactor name of the new plotting factor
#'
#' @examples
#' muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
#' package = "SpatialOmicsOverlay")))
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = as.factor(seq_len(length(sampNames(muBrain)))),
#' plottingFactor = "ROINum")
#'
#' head(plotFactors(muBrain))
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "factor",
function(overlay, annots, plottingFactor){
addPlottingFactor(overlay,
setNames(as.character(annots),
names(annots)),
plottingFactor)
})
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#' Add plotting factor to \code{\link{SpatialOverlay}} object
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots object with annotation: can be \code{NanoStringGeoMxSet},
#' \code{data.frame}, \code{matrix}, or vector containing
#' \code{character}, \code{factor}, or \code{numeric}
#' @param plottingFactor column or row from annots to add as plotting factor,
#' if using vector this will be the name of the new
#' plotting factor
#' @param ... if using \code{NanoStringGeoMxSet}, name of count matrix to pull
#' counts from
#'
#' @return \code{\link{SpatialOverlay}} object with new plotting factor
#'
#' @examples
#' muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
#' package = "SpatialOmicsOverlay")))
#'
#' muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt",
#' package = "SpatialOmicsOverlay")
#'
#' muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = muBrainLW,
#' plottingFactor = "segment")
#'
#' muBrainGxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip",
#' package = "SpatialOmicsOverlay")))
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = muBrainGxT,
#' plottingFactor = "Calm1",
#' countMatrix = "exprs")
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = seq_len(length(sampNames(muBrain))),
#' plottingFactor = "ROINum")
#'
#' head(plotFactors(muBrain))
#'
#' @export
#'
setGeneric("addPlottingFactor", signature = "annots",
function(overlay, annots, plottingFactor, ...)
standardGeneric("addPlottingFactor"))
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{NanoStringGeoMxSet} object
#' @param plottingFactor column or row from annots to add as plotting factor
#' @param countMatrix name of count matrix to pull counts from
#'
#' @export
#' @rdname addPlottingFactor
#'
#' @importFrom Biobase assayDataElement
#'
setMethod("addPlottingFactor", "NanoStringGeoMxSet",
function(overlay, annots, plottingFactor, countMatrix = "exprs"){
if(!is(overlay,"SpatialOverlay")){
stop("overlay must be a SpatialOverlay object")
}
if(length(plottingFactor) > 1){
warning("Plotting factors must be added 1 at a time, continuing with only the first factor")
plottingFactor <- plottingFactor[1]
}
if(is.null(plottingFactor)){
stop("Please provide valid plottingFactor")
}
if(!plottingFactor %in% colnames(sData(annots)) &
!plottingFactor %in% rownames(annots)){
stop("plottingFactor was not in given annots")
}
if(plottingFactor %in% colnames(sData(annots))){
axis <- "col"
}else{
axis <- "row"
}
samples <- sampNames(overlay)
gxtSamples <- gsub(".dcc", "", rownames(sData(annots)))
if(any(!samples %in% gxtSamples)){
sampIDs <- which(apply(as.matrix(sData(annots)), 2,
function(x){any(samples %in% x)}))
if(length(sampIDs) == 0){
stop("Sample IDs in SpatialOverlay do not match given annots")
}else if(length(sampIDs) > 1){
matchingSamps <- NULL
for(i in names(sampIDs)){
matchingSamps[i] <- length(sData(annots)[[i]] %in% samples)
}
sampIDs <- names(sort(matchingSamps, decreasing = TRUE)[1L])
}
gxtSamples <- sData(annots)[[sampIDs]]
}
annots <- annots[,match(samples, gxtSamples, nomatch = 0)]
gxtSamples <- gsub(".dcc", "", rownames(sData(annots)))
samples <- samples[match(gxtSamples, samples, nomatch = 0)]
if(length(samples) != length(sampNames(overlay))){
warning(paste("Missing annotations in annots. Samples missing:",
paste(sampNames(overlay)[!sampNames(overlay) %in%
samples],
collapse = ", ")))
overlay <- removeSample(overlay = overlay,
remove = sampNames(overlay)[which(!sampNames(overlay) %in%
samples)])
}
if(plottingFactor %in% colnames(plotFactors(overlay))){
if(axis == "col"){
overlay@plottingFactors[[plottingFactor]] <- sData(annots)[[plottingFactor]]
}else{
overlay@plottingFactors[[plottingFactor]] <- Biobase::assayDataElement(annots,
elt = countMatrix)[rownames(annots) ==
plottingFactor,]
}
}else{
if(axis == "col"){
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
sData(annots)[[plottingFactor]]))
}else{
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
Biobase::assayDataElement(annots,
elt = countMatrix)[rownames(annots) ==
plottingFactor,]))
}
rownames(overlay@plottingFactors) <- samples
colnames(overlay@plottingFactors)[ncol(plotFactors(overlay))] <- plottingFactor
}
if(is(plotFactors(overlay)[,ncol(plotFactors(overlay))], "character")){
overlay@plottingFactors[,ncol(plotFactors(overlay))] <- as.factor(plotFactors(overlay)[,ncol(plotFactors(overlay))])
}
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{matrix} containing plottingFactor, column or column names
#' must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "matrix",
function(overlay, annots, plottingFactor){
return(addPlottingFactor(annots = as.data.frame(annots),
overlay = overlay,
plottingFactor = plottingFactor))
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{matrix} containing plottingFactor, column or column names
#' must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "tbl_df",
function(overlay, annots, plottingFactor){
return(addPlottingFactor(annots = as.data.frame(annots),
overlay = overlay,
plottingFactor = plottingFactor))
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{matrix} containing plottingFactor, column or column names
#' must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "tbl",
function(overlay, annots, plottingFactor){
return(addPlottingFactor(annots = as.data.frame(annots),
overlay = overlay,
plottingFactor = plottingFactor))
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots \code{data.frame} containing plottingFactor, column or column
#' names must contian matching sample names to overlay
#' @param plottingFactor column or row name from annots to add as plotting
#' factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "data.frame",
function(overlay, annots, plottingFactor){
if(!is(overlay,"SpatialOverlay")){
stop("overlay must be a SpatialOverlay object")
}
if(length(plottingFactor) > 1){
warning("Plotting factors must be added 1 at a time, continuing with only the first factor")
plottingFactor <- plottingFactor[1]
}
if(is.null(plottingFactor)){
stop("Please provide valid plottingFactor")
}
if(!plottingFactor %in% colnames(annots) &
!plottingFactor %in% rownames(annots)){
stop("plottingFactor was not in given annots")
}
if(plottingFactor %in% colnames(annots)){
axis <- "col"
}else if(plottingFactor %in% rownames(annots)){
axis <- "row"
}else{
stop("plottingFactor must be in row or column names of annots")
}
samples <- sampNames(overlay)
if(axis == "col"){
sampIDs <- which(apply(annots, 2, function(x){any(samples %in%
x)}))
if(length(sampIDs) == 0){
stop("Sample IDs in SpatialOverlay do not match given annots")
}else if(length(sampIDs) > 1){
matchingSamps <- NULL
for(i in names(sampIDs)){
matchingSamps[i] <- length(annots[[i]] %in% samples)
}
sampIDs <- names(sort(matchingSamps, decreasing = TRUE)[1L])
}
annots <- annots[match(samples, annots[,sampIDs],
nomatch = 0),]
samples <- samples[match(annots[,sampIDs], samples,
nomatch = 0)]
}else{
annots <- annots[,match(samples, colnames(annots),
nomatch = 0)]
samples <- samples[match(colnames(annots), samples,
nomatch = 0)]
}
if(length(samples) != length(sampNames(overlay))){
warning(paste("Missing annotations in annots. Samples missing:",
paste(sampNames(overlay)[!sampNames(overlay) %in%
samples],
collapse = ", ")))
overlay <- removeSample(overlay = overlay,
remove = sampNames(overlay)[which(!sampNames(overlay) %in%
samples)])
}
if(plottingFactor %in% colnames(plotFactors(overlay))){
if(axis == "col"){
overlay@plottingFactors[[plottingFactor]] <- annots[[plottingFactor]]
}else{
overlay@plottingFactors[[plottingFactor]] <- t(annots[rownames(annots) ==
plottingFactor,])
}
}else{
if(axis == "col"){
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
annots[[plottingFactor]]))
}else{
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
t(annots[rownames(annots) ==
plottingFactor,])))
}
rownames(overlay@plottingFactors) <- samples
colnames(overlay@plottingFactors)[ncol(plotFactors(overlay))] <- plottingFactor
}
if(is(plotFactors(overlay)[,ncol(plotFactors(overlay))],"character")){
overlay@plottingFactors[,ncol(plotFactors(overlay))] <- as.factor(plotFactors(overlay)[,ncol(plotFactors(overlay))])
}
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots character vector with the plottingFactor. if names match sample
#' names in overlay vector will be matched on those,
#' otherwise assumed in the correct order
#' @param plottingFactor name of the new plotting factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "character",
function(overlay, annots, plottingFactor){
if(!is(overlay,"SpatialOverlay")){
stop("overlay must be a SpatialOverlay object")
}
if(is.null(plottingFactor)){
stop("Please provide valid plottingFactor")
}
if(is.null(names(annots))){
warning("No names on vector, assuming data is in same order as overlay",
immediate. = TRUE)
}
samples <- names(annots)
if(length(annots) < length(sampNames(overlay))){
if(is.null(names(annots))){
stop("Length of annots does not match samples in overlay & there are no names to match to")
}
warning(paste("Missing annotations in annots. Samples missing:",
paste(sampNames(overlay)[!sampNames(overlay) %in%
samples],
collapse = ", ")))
overlay <- removeSample(overlay = overlay,
remove = sampNames(overlay)[which(!sampNames(overlay) %in%
samples)])
}
samples <- sampNames(overlay)
if(plottingFactor %in% colnames(plotFactors(overlay))){
if(is.null(names(annots))){
annots <- annots[seq_len(length(samples))]
}else{
annots <- annots[match(samples, names(annots), nomatch = 0)]
samples <- samples[match(names(annots), samples, nomatch = 0)]
}
overlay@plottingFactors[[plottingFactor]] <- annots
}else{
if(!is.null(samples)){
if(is.null(names(annots))){
annots <- annots[seq_len(length(samples))]
}else{
annots <- annots[match(samples, names(annots), nomatch = 0)]
samples <- samples[match(names(annots), samples, nomatch = 0)]
}
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
annots))
}else{
overlay@plottingFactors <- as.data.frame(cbind(plotFactors(overlay),
t(annots)))
}
rownames(overlay@plottingFactors) <- samples
colnames(overlay@plottingFactors)[ncol(plotFactors(overlay))] <- plottingFactor
}
if(is(plotFactors(overlay)[,ncol(plotFactors(overlay))],"character")){
overlay@plottingFactors[,ncol(plotFactors(overlay))] <-
as.factor(plotFactors(overlay)[,ncol(plotFactors(overlay))])
}
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots numeric vector with the plottingFactor. if names match sample
#' names in overlay vector will be matched on those,
#' otherwise assumed in the correct order
#' @param plottingFactor name of the new plotting factor
#'
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "numeric",
function(overlay, annots, plottingFactor){
overlay <- addPlottingFactor(overlay,
setNames(as.character(annots),
names(annots)),
plottingFactor)
overlay@plottingFactors[,ncol(plotFactors(overlay))] <- as.numeric(as.character(plotFactors(overlay)[,ncol(plotFactors(overlay))]))
return(overlay)
})
#'
#'
#' @param overlay \code{\link{SpatialOverlay}} object
#' @param annots factor vector with the plottingFactor. if names match sample
#' names in overlay vector will be matched on those,
#' otherwise assumed in the correct order
#' @param plottingFactor name of the new plotting factor
#'
#' @examples
#' muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
#' package = "SpatialOmicsOverlay")))
#'
#' muBrain <- addPlottingFactor(overlay = muBrain,
#' annots = as.factor(seq_len(length(sampNames(muBrain)))),
#' plottingFactor = "ROINum")
#'
#' head(plotFactors(muBrain))
#' @export
#' @rdname addPlottingFactor
#'
setMethod("addPlottingFactor", "factor",
function(overlay, annots, plottingFactor){
addPlottingFactor(overlay,
setNames(as.character(annots),
names(annots)),
plottingFactor)
})
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