AbNames: Standardize Antibody Names

# renameADT generic ----
#'
#'Replace ADT names in an object containing ADT expression
#'
#'@description
#'Given an object containing antibody derived tag (ADT) expression measurements,
#'such as a [SingleCellExperiment::SingleCellExperiment()] or
#'[MultiAssayExperiment::MultiAssayExperiment()] and a vector of new names,
#'replace the names of the ADTs and store the original names as metadata.
#'
#' Used for e.g. standardising protein names across studies.  See
#' `getCommonName()` for generating standardised names by matching to the
#' citeseq data set. Names have to be provided because we recommend manually
#' checking standard names.
#'@param obj An object containing ADT expression measurements
#'@param names A character vector of new names, equal to the number of ADTs
#'in obj
#'@param ... Not currently used
#'@returns An object of the same class as obj, with ADT measurements renamed
#'@author Helen Lindsay
#'@importFrom methods setGeneric
#'@export
#'@rdname renameADT-methods
setGeneric("renameADT", signature=c("obj", "names"),
           function(obj, names, ...) {
    standardGeneric("renameADT")
})


# renameADT for signature SingleCellExperiment ------
#'@param assay Name of the assay to be renamed (Default: "counts")
#'@importFrom methods setMethod signature
#'@export
#'@rdname renameADT-methods
setMethod("renameADT", as(structure(.Data = c("SingleCellExperiment",
                                              "character"),
                                    names = c("obj", "names"),
                                    package = c("SingleCellExperiment", "")),
                          "signature"),
    function(obj, names, assay = "ADT", ...) {
        # to do - add old names to row data

        # names = named vector of new names, names are current names

        # For a SingleCellExperiment, the ADT may either be the main assay
        # or an altExp.

        # sce may have rowPairs, but doesn't appear to inc names
        # check rownames of rowdata

        stopifnot(requireNamespace("SummarizedExperiment"),
                  requireNamespace("SingleCellExperiment"))

        main_assay_name <- names(SummarizedExperiment::assays(obj))
        is_alt <- assay %in% SingleCellExperiment::altExpNames(obj)

        if (is_alt){
            # Swap ADT assay to be the main assay
            obj <- SingleCellExperiment::swapAltExp(obj, assay,
                                                    saved = main_assay_name)
        }

        # Make sure new names vector has names
        if (is.null(names(names))){
            names(names) <- rownames(obj)
        }

        if (! all(names(names) %in% rownames(obj))){
            stop("If names is a named vector, all names ",
                 "must be rownames of required assay in obj")
        }

        # Update names - use coalesce in case there are missing values
        old_nms <- rownames(obj)
        new_nms <- dplyr::coalesce(names[rownames(obj)], old_nms)
        rownames(obj) <- new_nms

        # Put old names into row data
        SummarizedExperiment::rowData(obj) <-
            cbind(SummarizedExperiment::rowData(obj),
                  S4Vectors::DataFrame(Original_Names = old_nms))

        if (is_alt){
            # Swap ADT back to being an altExp
            obj <- SingleCellExperiment::swapAltExp(obj, main_assay_name,
                                                    saved = assay)
        }

        return(obj)
})


# renameADT for signature MultiAssayExperiment ------
# https://stackoverflow.com/questions/57380044/
# how-to-document-s4-methods-that-rely-on-classes-from-external-packages
#'@rdname renameADT-methods
setMethod("renameADT", as(structure(.Data = c("MultiAssayExperiment",
                                              "character"),
                                     names = c("obj", "names"),
                                     package = c("MultiAssayExperiment", "")),
                          "signature"),
    function(obj, names, assay = "counts", ...) {
        stopifnot(requireNamespace("SummarizedExperiment"),
                  requireNamespace("MultiAssayExperiment"))
        nms <- rownames(SingleCellExperiment::experiments(obj)[[assay]])
        #nms <- .getRownames(obj, assay)
})


# # renameADT for signature Seurat ------
# #'@importFrom methods slotNames slot
# setMethod("renameADT", signature(obj = "Seurat",
#                                  assay = "character"),
#     function(obj, assay) {
#         stopifnot(requireNamespace("Seurat"),
#                   requireNamespace("SeuratObject"))
#
#         if (! assay %in% Assays(obj)){
#             stop(sprintf("Assay %s not found.\n  Available assays: %s\n",
#                          assay, toString(SeuratObject::Assays(obj))))
#         }
#
#         # To do: add Seurat, SeuratObject to suggests
#         # Names might also have to be changed in "reductions"?
#         # (not in Triana_2022, maybe in others)
#
#         # Can rownames be updated just with rownames?
#         # Or convert to SingleCellExperiment and back?
#
#
#         # Find slots in the Assay object that have to be changed
#         sr_assay <- obj@assays[[assay]]
#         assay_slots <- slotNames(sr_assay)
#         assay_has_rn <- vapply(assay_slots, function(nm){
#             ! is.null(rownames(slot(sr_assay, nm)))
#             }, logical(1))
#
#         # https://github.com/satijalab/seurat/issues/1049
#         # https://github.com/mojaveazure/seurat-object/issues/3
#         #obj@assays$RNA@counts@Dimnames[[1]] <- mgi$genes
#         #obj@assays$RNA@data@Dimnames[[1]] <- mgi$genes
#         #obj@assays$RNA@meta.features <- mgi
#
#         # modify counts, data and scale.data slots for every assay
#         # you have in your Seurat object. In addition, you will also
#         # need to modify the meta.data slots for both the object and
#         # each assay object contained within the Seurat object.
#         # Finally, you'll need to rerun any dimensional reduction
#         # and graph-building (eg. FindNeighbors)
#
#         # RenameGenesSeurat <- function(obj = ls.Seurat[[i]],
#          newnames = HGNC.updated[[i]]$Suggested.Symbol) {
#        #Replace gene names in different slots of a Seurat object.
#       #Run this before integration. Run this before integration.
# #It only changes obj@assays$RNA@counts, @data and @scale.data.
#         #print("Run this before integration. It only changes
# #obj@assays$RNA@counts, @data and @scale.data.")
#         #RNA <- obj@assays$RNA
#
#         #if (nrow(RNA) == length(newnames)) {
#         #    if (length(RNA@counts)) RNA@counts@Dimnames[[1]]    <- newnames
#         #    if (length(RNA@data)) RNA@data@Dimnames[[1]]        <- newnames
#         #    if (length(RNA@scale.data)) RNA@scale.data@Dimnames[[1]]
#         # <- newnames
#         #} else {"Unequal gene sets: nrow(RNA) != nrow(newnames)"}
#         #obj@assays$RNA <- RNA
#         #return(obj)
#     #}
#
# })