R/show-methods.R

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

#' Show function for \code{compData} object
#' 
#' Show function for \code{compData} object. 
#' @param object A \code{compData} object
#' 
#' @keywords internal
#' 
show_compData <- function(object) {
  nbr.random.outliers <- 
    sum(object@variable.annotations$n.random.outliers.up.S1 + 
          object@variable.annotations$n.random.outliers.down.S1 + 
          object@variable.annotations$n.random.outliers.up.S2 + 
          object@variable.annotations$n.random.outliers.down.S2)
  nbr.single.outliers <- 
    sum(object@variable.annotations$n.single.outliers.up.S1 + 
          object@variable.annotations$n.single.outliers.down.S1 + 
          object@variable.annotations$n.single.outliers.up.S2 + 
          object@variable.annotations$n.single.outliers.down.S2)
  nbr.diffexp <- sum(object@variable.annotations$differential.expression)
  if (length(object@method.names) == 0) {
    diffexp.statement <- "No differential expression analysis has been performed."
  } else {
    diffexp.statement <- 
      paste("Differential expression analysis was performed by the method", 
            object@method.names$full.name, "on", 
            object@analysis.date, ".")
  }
  cat(paste("An object of class", class(object), "\n"))
  cat(paste("Dataset name:", object@info.parameters$dataset, "\n"))
  cat(paste("Number of samples:", ncol(object@count.matrix), "\n"))
  cat(paste("Number of variables:", nrow(object@count.matrix), "\n"))
  cat(paste("Number of random outliers:", nbr.random.outliers, "\n"))
  cat(paste("Number of single outliers:", nbr.single.outliers, "\n"))
  cat(paste("Number of known truly differentially expressed genes:", nbr.diffexp, "\n"))
  cat(paste(diffexp.statement, "\n\n"))
  cat("count.matrix:\n")
  print(utils::head(object@count.matrix[, seq_len(min(ncol(object@count.matrix), 6))]))
  nbrleftoutrows <- max(c(0, nrow(object@count.matrix) - 6))
  nbrleftoutcols <- max(c(0, ncol(object@count.matrix) - 6))
  if (nbrleftoutrows > 0 & nbrleftoutcols > 0) {
    cat(paste("+", nbrleftoutrows, "rows and", nbrleftoutcols, "cols...\n\n"))
  } else if (nbrleftoutrows > 0) {
    cat(paste("+", nbrleftoutrows, "rows...\n\n"))
  } else if (nbrleftoutcols > 0) {
    cat(paste("+", nbrleftoutrows, "cols...\n\n"))
  }
  cat("sample.annotations:\n")
  print(utils::head(object@sample.annotations))
  nbrleftoutrows <- max(c(0, nrow(object@sample.annotations) - 6))
  if (nbrleftoutrows > 0) {
    cat(paste("+", nbrleftoutrows, "rows...\n\n"))
  } else {
    cat("\n")
  }
  cat("variable.annotations:\n")
  print(utils::head(object@variable.annotations))
  nbrleftoutrows <- max(c(0, nrow(object@variable.annotations) - 6))
  if (nbrleftoutrows > 0) {
    cat(paste("+", nbrleftoutrows, "rows...\n\n"))
  } else {
    cat("\n")
  }
  
  if (length(object@method.names) != 0) {
    cat("Differential expression results:\n\n")
    print(utils::head(object@result.table))
    nbrleftoutrows <- max(c(0, nrow(object@result.table) - 6))
    if (nbrleftoutrows > 0) {
      cat(paste("+", nbrleftoutrows, "rows...\n\n"))
    } else {
      cat("\n")
    }
  }
}

#' Show method for \code{compData} object
#' 
#' Show method for \code{compData} object. 
#' @param object A \code{compData} object
#' @author Charlotte Soneson
#' @examples 
#' mydata <- generateSyntheticData(dataset = "mydata", n.vars = 12500, 
#'                                 samples.per.cond = 5, n.diffexp = 1250)
#' mydata
#' @importFrom utils head
setMethod(
  f = "show",  # name of function
  signature = "compData",  # class of each argument. other ex: signature = c(x = , y = )
  definition = show_compData
)

#' Show method for \code{phyloCompData} object
#' 
#' Show method for \code{phyloCompData} object. 
#' @param object A \code{phyloCompData} object
#' @author Charlotte Soneson, Paul Bastide
#' @examples 
#' mydata <- generateSyntheticData(dataset = "mydata", n.vars = 1000, 
#'                                 samples.per.cond = 5, n.diffexp = 100,
#'                                 id.species = factor(1:10),
#'                                 tree = ape::rphylo(10, 1, 0),
#'                                 lengths.relmeans = "auto", lengths.dispersions = "auto")
#' mydata
#' @importFrom utils head
setMethod(
  f = "show",  # name of function
  signature = "phyloCompData",  # class of each argument. other ex: signature = c(x = , y = )
  definition = function(object) {
    show_compData(object)

    if (length(object@tree) != 0) {
      cat("Phylogenetic tree:\n")
      print(object@tree)
      cat("\n")
    } else {
      cat("Without phylogenetic tree. \n")
    }
    
    if (length(object@length.matrix) != 0) {
      cat("length.matrix:\n")
      print(head(object@length.matrix[, 1:min(ncol(object@length.matrix), 6)]))
      cat("\n")
    } else {
      cat("No length matrix. \n")
    }
  }
)

#setGeneric("show")