metPath: Pathway analysis for metabolomics data

#' #' @title creatMetPathObject
#' #' @description Creat metPathClass object.
#' #' @author Xiaotao Shen
#' #' \email{shenxt@@sioc.ac.cn}
#' #' @param ms1.data MS1 peak table name.
#' #' @param sample.information Sample information name.
#' #' @param path Work directory.
#' #' @return A metPathClass object.
#' #' @export
#' 
#' setGeneric(
#'   name = "creatMetPathObject",
#'   def = function(ms1.data,
#'                  sample.information,
#'                  path = ".") {
#'     check.result <- checkData(data = ms1.data,
#'                               sample.info = sample.information,
#'                               path = path)
#' 
#'     if (any(check.result$`Check result` != "Valid")) {
#'       stop("Error is in you data. Please check it.\n")
#'     }
#' 
#'     ms1.data.name <- ms1.data
#'     sample.information.name <- sample.information
#' 
#'     ms1.data <- pbapply::pblapply(ms1.data, function(x) {
#'       readr::read_csv(file = file.path(path, x),
#'                       col_types = readr::cols())
#'     })
#' 
#'     sample.info <-
#'       readr::read_csv(file.path(path, sample.information),
#'                       col_types = readr::cols())
#' 
#'     object <- new(
#'       Class = "metPathClass",
#'       ms1.data = ms1.data,
#'       sample.info = sample.info,
#'       version = "0.1.0"
#'     )
#'     invisible(object)
#'   }
#' )
#' 
#' 
#' #' An S4 class to represent a metPath object.
#' #'
#' #' @slot ms1.data MS1 data.
#' #' @slot sample.info Sample information.
#' #' @slot process.info MS1 data.
#' #' @slot version MS1 data.
#' 
#' ##S4 class for function metIdentification
#' setClass(
#'   Class = "metPathClass",
#'   representation(
#'     ms1.data = "list",
#'     sample.info = "data.frame",
#'     process.info = "list",
#'     version = "character"
#'   )
#' )
#' 
#' setMethod(
#'   f = "show",
#'   signature = "metPathClass",
#'   definition = function(object) {
#'     # requireNamespace("magrittr")
#'     cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
#'     cat(crayon::green("metPath version:", object@version, "\n"))
#'     cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
#'     cat(crayon::green("MS1 data\n"))
#'     cat("There are",
#'         length(object@ms1.data),
#'         "peak tables in your MS1 data.\n")
#'     info <- lapply(object@ms1.data, dim) %>%
#'       do.call(rbind, .)
#' 
#'     colnames(info) <- c("Peak.number", "Column.number")
#'     rownames(info) <- paste("Batch", 1:nrow(info), sep = "")
#'     print(info)
#'     cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
#'     cat("There are",
#'         nrow(object@sample.info),
#'         "samples in your MS1 data.\n")
#'     class_info <-
#'       as.data.frame(table(object@sample.info$class), stringsAsFactors = FALSE)
#'     colnames(class_info) <- c("Class", "Number")
#'     print(class_info)
#'     cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
#'     group_info <-
#'       as.data.frame(table(object@sample.info$group), stringsAsFactors = FALSE)
#'     colnames(group_info) <- c("Group", "Number")
#'     print(group_info)
#'     cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
#'     cat(crayon::green("Processing\n"))
#'     if (.hasSlot(object = object, name = "process.info") &
#'         length(object@process.info) != 0) {
#'       process.info <- object@process.info
#'       mapply(function(x, y) {
#'         cat(crayon::green(x, paste(rep("-", 10), collapse = ""), "\n"))
#'         y <- y[which(names(y) != "plot")]
#'         y <- data.frame(names(unlist(y)), unlist(y))
#'         colnames(y) <- c("Parameter", "Value")
#'         rownames(y) <- NULL
#'         print(y)
#'       },
#'       x = names(process.info),
#'       y = process.info)
#'     } else{
#'       cat(crayon::red("There are no processing for your data.\n"))
#'     }
#'   }
#' )