R/ClassDataElement.R

In jwist/fusion: Fusion: Objects class definitions for metabolic profiling

#' An S4 class for dataElement
#'
#' @slot .Data the data matrix
#' @slot varName a vector containing the name of each variable
#' @slot obsDescr a data.frame containing experimental
#' conditions and a field called sampleID that MUST be unique.
#' @slot method a name for the method used to acquire the data
#' @slot type type can be of type (See meltdown())
#' @slot version versioning
#' @return a dataElement
#' @export
#' @importFrom crayon %+%

setClass("dataElement",
  representation = representation(
    .Data = "matrix",
    varName = "character",
    obsDescr = "list",
    type = "character",
    method = "character",
    version = "character"
  ),
  prototype(
    varName = NA_character_,
    obsDescr = data.frame(),
    method = NA_character_,
    type = NA_character_,
    version = NA_character_
  ),
  validity = function(object) {
    if (is.na(object@type)) {
      stop(crayon::red("fusion:ClassDataElement >> a type must be given"))
    }
    supportedTypes <- c(
      "NMR",
      "U-MS",
      "T-MS",
      "ANN",
      "MRMS"
    )
    if (!object@type %in% supportedTypes) {
      cat("supportedTypes:", supportedTypes, "\n")
      stop(crayon::red("fusion:ClassDataElement >> unsupported type"))
    }

    if (object@type == "NMR" & is.na(object@method)) {
      stop(crayon::red("fusion:ClassDataElement >> fusion: NMR dataElement must
      contain a valid method\nUse meltdown() to check for valid types"))

      if (!object@method %in% meltdown()$NMR$method) {
        stop(crayon::red("fusion:ClassDataElement >> fusion: NMR dataElement
        must contain a method\nUse meltdown() to check for valid types"))
      }
    }

    if (object@type == "T-MS" & is.na(object@method)) {
      stop(crayon::red("fusion:ClassDataElement >> fusion: T-MS dataElement must
      contain a method\nUse meltdown() to check for valid types"))

      if (!object@method %in% meltdown()["T-MS"][[1]]$method) {
        stop(crayon::red("fusion:ClassDataElement >> fusion: T-MS dataElement
        must contain a method\nUse meltdown() to check for valid types"))
      }
    }

    if (object@type == "QUANT" & is.na(object@method)) {
      stop(crayon::red("fusion:ClassDataElement >> fusion: QUANT dataElement
      mustcontain a method\nUse meltdown() to check for valid types"))

      if (!object@method %in% meltdown()["QUANT"][[1]]$method) {
        stop(crayon::red("fusion:ClassDataElement >> fusion: QUANT dataElement
        must contain a method\nUse meltdown() to check for valid types"))
      }
    }

    if (object@type == "ANN" & any(
      !is.na(object@method),
      !is.na(object@varName),
      !is.na(object@.Data)
    )) {
      stop(crayon::red("fusion:ClassDataElement >>
      fusion: ANN dataElement must not contain a method, a varName or .Data"))
    }
    if (!is.list(object@obsDescr)) {
      stop(crayon::red("fusion:ClassDataElement >>
      fusion: obsDescr must be of type list"))
    }

    meta <- object@obsDescr[[1]]
    if ("sampleID" %in% names(meta)) {
      if (object@type != "ANN") {
        fi <- getType(object) == "sample"
        ids <- getID(object)[fi]
      } else {
        ids <- getID(object)
      }
      if (sum(duplicated(ids)) > 0) {
        stop(crayon::red("fusion:ClassDataElement >> the sampleID (for type of
        samples) are not unique"))
      }
    } else {
      stop(crayon::red("fusion:ClassDataElement >> the metadata must contain
      a column: sampleID"))
    }

    if (!"dataPath" %in% names(meta) & object@type %in% c("NMR", "QUANT")) {
      stop(crayon::red("fusion:ClassDataElement >> NMR & QUANT metadata must
      contain a column: dataPath"))
    }

    if (object@type != "ANN") {
      if ("sampleType" %in% names(meta)) {
        cat(crayon::green(names(table(meta$sampleType))) %+%
          crayon::green(": ") %+%
          crayon::green(table(meta$sampleType)), fill = 2)
      } else {
        stop(crayon::red("fusion:ClassDataElement >> the metadata must contain
     a column: sampleType"))
      }
    }
    return(check(object))
  },
  contains = list("matrix")
)