R/AllClasses.R

In shmohammadi86/ACTIONetExperiment: ACTIONetExperiment container object

#' An extension of the SummarizedExperiment class to store
#' the results of ACTIONet method
#'
#' @slot rowNets,colNets gene-gene and cell-cell networks, respectively
#' @slot rowMaps,colMaps Factorization results (W and H matrices)
#'
#'
#' @return an ACTIONetExperiment (ACE) object
#' @rdname ACTIONetExperiment
#' @import methods
#' @importFrom stats setNames
#' @importClassesFrom S4Vectors SimpleList
#' @importClassesFrom SummarizedExperiment RangedSummarizedExperiment
setClass(
  "ACTIONetExperiment",
  slots = c(
    rowNets = "SimpleList",
    colNets = "SimpleList",
    rowMaps = "SimpleList",
    colMaps = "SimpleList"
  ),
  contains = "RangedSummarizedExperiment"
)


#' Creates an ACTIONetExperiment (ACE) object
#'
#' @param ... SummarizedExperiment and SummarizedExperiment components
#' @param rowNets,colNets gene-gene and cell-cell networks, respectively
#' @param rowMaps,colMaps Factorization results (W and H matrices)
#'
#' @return An ACTIONetExperiment (ACE) object, derived from SummarizedExperiment, with additional slots to store ACTIONet results
#' @importFrom methods new
#' @importFrom S4Vectors SimpleList
#' @importClassesFrom SummarizedExperiment RangedSummarizedExperiment
#' @export
ACTIONetExperiment <- function(
  ...,
  rowNets = S4Vectors::SimpleList(),
  colNets = S4Vectors::SimpleList(),
  rowMaps = S4Vectors::SimpleList(),
  colMaps = S4Vectors::SimpleList()
) {

    SE <- SummarizedExperiment::SummarizedExperiment(...)

    if (!is(SE, "RangedSummarizedExperiment")) {
        SE <- as(SE, "RangedSummarizedExperiment")
    }

    out = new("ACTIONetExperiment", SE, rowNets = rowNets, colNets = colNets)
    out = .insert_mapping(out, rowMaps, 1)
    out = .insert_mapping(out, colMaps, 2)

    if (NROW(out) > 0) {
        # if(NCOL(SummarizedExperiment::rowData(out)) == 0){
        # SummarizedExperiment::rowData(out) = .default_rowData(NROW(out)) rownames(out)
        # = SummarizedExperiment::rowData(out)[,1] %>% .make_chars_unique }
        # if(is.null(rownames(SummarizedExperiment::rowData(out)))){ rownames(out) =
        # SummarizedExperiment::rowData(out)[,1] %>% .make_chars_unique } else {
        # rownames(out) = rownames(SummarizedExperiment::rowData(out)) %>%
        # .make_chars_unique }
        if (is.null(rownames(out))) {
            rownames(out) = .default_rownames(NROW(out))
        }
    }

    if (NCOL(out) > 0) {
        # if(NCOL(SummarizedExperiment::colData(out)) == 0){
        # SummarizedExperiment::colData(out) = .default_colData(NCOL(out)) colnames(out)
        # = SummarizedExperiment::colData(out)[,1] %>% .make_chars_unique }
        # if(is.null(rownames(SummarizedExperiment::colData(out)))){ colnames(out) =
        # SummarizedExperiment::colData(out)[,1] %>% .make_chars_unique } else {
        # colnames(out) = rownames(SummarizedExperiment::colData(out)) %>%
        # .make_chars_unique }
        if (is.null(colnames(out))) {
            colnames(out) = .default_colnames(NCOL(out))
        }
    }

    validObject(out)
    return(out)
}


# @S3method .DollarNames ACTIONetExperiment
#' @method .DollarNames ACTIONetExperiment
#' @export
.DollarNames.ACTIONetExperiment <- function(
  x,
  pattern = ""
) {

    ll = c(
      names(colData(x)),
      names(rowMaps(x, all = F)),
      names(colMaps(x, all = F)),
      names(colNets(x)),
      names(rowNets(x))
    )

    out = grep(pattern, ll, value = TRUE)
    out
}

#' @export
setMethod(".DollarNames", "ACTIONetExperiment", .DollarNames.ACTIONetExperiment)


#' @export
setMethod("$", "ACTIONetExperiment", function(x, name) {

    if (name %in% names(colData(x))) {
        colData(x)[[name]]
    } else if (name %in% names(rowMaps(x, all = F))) {
        rowMaps(x)[[name]]
    } else if (name %in% names(colMaps(x, all = F))) {
        colMaps(x)[[name]]
    } else if (name %in% names(colNets(x))) {
        colNets(x)[[name]]
    } else if (name %in% names(rowNets(x))) {
        rowNets(x)[[name]]
    } else {
        message(sprintf("Attribute %s not found", name))
    }

})


#' @export
setReplaceMethod("$", "ACTIONetExperiment", function(x, name, value) {
    if (name %in% names(colData(x))) {
        colData(x)[[name]] <- value
    } else if (name %in% names(rowMaps(x))) {
        rowMaps(x)[[name]] <- value
    } else if (name %in% names(colMaps(x))) {
        colMaps(x)[[name]] <- value
    } else if (name %in% names(colNets(x))) {
        colNets(x)[[name]] <- value
    } else if (name %in% names(rowNets(x))) {
        rowNets(x)[[name]] <- value
    } else {
        colData(x)[[name]] <- value
    }

    x
})