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S3 method consistency for seurat v5 SetAssayData
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@timoast
timoast committed Nov 6, 2023
1 parent 4015810 commit 74bad58
Showing 1 changed file with 37 additions and 27 deletions.
64 changes: 37 additions & 27 deletions R/objects.R
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Original file line number Diff line number Diff line change
Expand Up @@ -764,26 +764,36 @@ RenameCells.Fragment <- function(object, new.names, ...) {

#' @importFrom SeuratObject SetAssayData
#' @importFrom GenomeInfoDb genome Seqinfo
#' @importFrom lifecycle deprecated is_present
#' @method SetAssayData ChromatinAssay
#' @concept assay
#' @export
SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
if (!(slot %in% slotNames(x = object))) {
SetAssayData.ChromatinAssay <- function(
object,
layer,
new.data,
slot = deprecated(),
...
) {
if (is_present(arg = slot)) {
layer <- slot
}
if (!(layer %in% slotNames(x = object))) {
stop(
"slot must be one of ",
"layer must be one of ",
paste(slotNames(x = object), collapse = ", "),
call. = FALSE
)
}
if (slot %in% c("counts", "data", "scale.data")) {
if (layer %in% c("counts", "data", "scale.data")) {
if (!(is(object = new.data, class2 = "AnyMatrix"))) {
stop("Data must be a matrix or sparseMatrix")
}
if (ncol(x = object) != ncol(x = new.data)) {
stop("Number of columns in the provided matrix does not match
the number of cells in the object")
}
if (slot %in% c("counts", "data")) {
if (layer %in% c("counts", "data")) {
if (nrow(x = object) != nrow(x = new.data)) {
stop("Number of rows in provided matrix does not match
the number of rows in the object")
Expand All @@ -795,19 +805,19 @@ SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
the number of rows in the object")
}
}
slot(object = object, name = slot) <- new.data
} else if (slot == "seqinfo") {
slot(object = object, name = layer) <- new.data
} else if (layer == "seqinfo") {
if (inherits(x = new.data, what = "Seqinfo")) {
slot(object = object, name = slot) <- new.data
slot(object = object, name = layer) <- new.data
} else if (is(object = new.data, class2 = "character")) {
slot(object = object, name = slot) <- Seqinfo(genome = new.data)
slot(object = object, name = layer) <- Seqinfo(genome = new.data)
} else if(is.null(x = new.data)) {
slot(object = object, name = slot) <- NULL
slot(object = object, name = layer) <- NULL
} else {
stop("Unknown object supplied. Choose a Seqinfo object or the name
of a UCSC genome")
}
} else if (slot == "fragments") {
} else if (layer == "fragments") {
if (inherits(x = new.data, what = "list")) {
# check that it's a list containing fragment class objects
for (i in seq_along(new.data)) {
Expand All @@ -819,7 +829,7 @@ SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
# single fragment object
new.data <- list(new.data)
}
frag.list <- GetAssayData(object = object, slot = "fragments")
frag.list <- GetAssayData(object = object, layer = "fragments")
if (length(x = frag.list) != 0) {
warning("Overwriting existing fragment objects")
}
Expand All @@ -836,23 +846,23 @@ SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
stop("Annotation genome does not match genome of the object")
}
}
slot(object = object, name = slot) <- new.data
} else if (slot == "bias") {
slot(object = object, name = layer) <- new.data
} else if (layer == "bias") {
if (!is(object = new.data, class2 = "vector")) {
stop("Bias must be provided as a vector")
}
slot(object = object, name = slot) <- new.data
} else if (slot == "positionEnrichment") {
slot(object = object, name = layer) <- new.data
} else if (layer == "positionEnrichment") {
if (inherits(x = new.data, what = "list")) {
# list of position enrichment matrices being added
if (length(x = new.data) == 0) {
# if list is empty, assign and overwrite slot
slot(object = object, name = slot) <- new.data
slot(object = object, name = layer) <- new.data
} else if (is.null(x = names(x = new.data))) {
stop("If supplying a list of position enrichment matrices,
each element must be named")
} else {
current.data <- GetAssayData(object = object, slot = slot)
current.data <- GetAssayData(object = object, layer = layer)
if (length(x = current.data) != 0) {
warning("Overwriting current list of position enrichement matrices")
}
Expand All @@ -863,7 +873,7 @@ SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
)
}
}
slot(object = object, name = slot) <- new.data
slot(object = object, name = layer) <- new.data
}
} else if (!is(object = new.data, class2 = "AnyMatrix")) {
stop("Position enrichment must be provided as a matrix or sparseMatrix")
Expand All @@ -875,19 +885,19 @@ SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
} else {
key <- args$key
}
current.pos <- slot(object = object, name = slot)
current.pos <- slot(object = object, name = layer)
current.pos[[key]] <- new.data
slot(object = object, name = slot) <- current.pos
slot(object = object, name = layer) <- current.pos
}
} else if (slot == "ranges") {
} else if (layer == "ranges") {
if (!is(object = new.data, class2 = "GRanges")) {
stop("Must provide a GRanges object")
} else if (length(x = new.data) != nrow(x = object)) {
stop("Number of ranges provided is not equal to the number
of features in the assay")
}
slot(object = object, name = slot) <- new.data
} else if (slot == "motifs") {
slot(object = object, name = layer) <- new.data
} else if (layer == "motifs") {
if (!inherits(x = new.data, what = "Motif")) {
stop("Must provide a Motif class object")
}
Expand All @@ -906,9 +916,9 @@ SetAssayData.ChromatinAssay <- function(object, slot, new.data, ...) {
new.data <- new.data[keep.features, ]
}
}
slot(object = object, name = slot) <- new.data
} else if (slot == "links") {
slot(object = object, name = slot) <- new.data
slot(object = object, name = layer) <- new.data
} else if (layer == "links") {
slot(object = object, name = layer) <- new.data
}
return(object)
}
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