R/T.value.R

In adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data

setClass(
  Class = "T.value",
  contains = "ADEg.T"
)


setMethod(
  f = "prepare",
  signature = "T.value",
  definition = function(object) {
    name_obj <- deparse(substitute(object))
    
    ## pre-management of graphics parameters      
    oldparamadeg <- adegpar()
    on.exit(adegpar(oldparamadeg))
    adegtot <- adegpar(object@adeg.par)
    
    if(object@data$storeData) {
      z <- as.vector(as.matrix(object@data$dftab))
      dftab <- object@data$dftab
      labelsx <- object@data$labelsx
      labelsy <- object@data$labelsy
    } else {
      z <- as.vector(as.matrix(eval(object@data$dftab, envir = sys.frame(object@data$frame))))
      dftab <- eval(object@data$dftab, envir = sys.frame(object@data$frame))
      labelsx <- eval(object@data$labelsx, envir = sys.frame(object@data$frame))
      labelsy <- eval(object@data$labelsy, envir = sys.frame(object@data$frame))
    }
    
    if(is.null(object@g.args$breaks))
      object@s.misc$breaks.update <- pretty(z, object@g.args$nclass)
    else
      object@s.misc$breaks.update <- object@g.args$breaks
    
    object@s.misc$breaks.update <- breakstest(object@s.misc$breaks.update, z, n = length(object@s.misc$breaks.update))
    n <- length(object@s.misc$breaks.update)
    
    if(is.null(object@adeg.par$ppoints$cex))
      adegtot$ppoints$cex <- 1
    
    if(is.null(object@adeg.par$ppoints$alpha))
      adegtot$ppoints$alpha <- 1
    
    if(is.null(labelsx))
      adegtot$ptable$x$tck <- 0
    if(is.null(labelsy))
      adegtot$ptable$y$tck <- 0
    
    ## symbols for z = center
    if(!is.null(object@g.args$centerpar)) {
      default <- list(pch = 4, cex = 1, col = "black")
      if(is.list(object@g.args$centerpar))
        object@g.args$centerpar <- modifyList(default, object@g.args$centerpar, keep.null = TRUE)
      else
        object@g.args$centerpar <- default
    }
    
    ## setting colors
    if(!is.null(object@g.args$col)) {
      switch(object@g.args$method,
             size = {
               if(length(object@g.args$col) != 2 & !inherits(dftab, "table") & !inherits(dftab, "dist"))
                 stop("if method size choosen, col vector should be size 2", call. = FALSE)
               adegtot$ppoints$col <- object@g.args$col ## color given by the user
             },
             color = {
               if(length(object@g.args$col) < (n - 1))
                 stop(paste("not enough colors defined for method color, at least ", (n - 1), " colors expected", sep = "") , call. = FALSE)
               adegtot$ppoints$fill <- object@g.args$col[1:(n - 1)] ## color given by the user
             })
    } else {
      if(object@g.args$method == "color")
        adegtot$ppoints$fill <- adegtot$ppalette$quanti(n - 1)
      else if(inherits(dftab, "table") | inherits(dftab, "dist")) {
        adegtot$ppoints$col <- adegtot$ppalette$quanti(2)
      }
      else
        adegtot$ppoints$col <- adegtot$ppalette$quanti(2)
    }
    
    ## object modification before calling inherited method
    object@adeg.par <- adegtot
    callNextMethod() ## prepare graph
    
    assign(name_obj, object, envir = parent.frame())
  })


setMethod(
  f = "panel",
  signature = "T.value",
  definition = function(object, x, y) {
    if(object@data$storeData)
      dftab <- as.matrix(object@data$dftab)
    else
      dftab <- as.matrix(eval(object@data$dftab, envir = sys.frame(object@data$frame)))
    adeg.panel.values(x = x[col(dftab)], y = y[row(dftab)], z = as.vector(dftab), center = object@g.args$center, method = object@g.args$method,
                      symbol = object@g.args$symbol, ppoints = object@adeg.par$ppoints, breaks = object@s.misc$breaks.update, centerpar = object@g.args$centerpar)
  })


table.value <- function(dftab, coordsx = 1:ncol(as.matrix(dftab)), coordsy = nrow(as.matrix(dftab)):1, labelsx, labelsy, breaks = NULL, method = c("size", "color"),
                        symbol = c("square", "circle", "diamond", "uptriangle", "downtriangle"), col = NULL, nclass = 3, center = 0, centerpar = NULL, plot = TRUE,
                        storeData = TRUE, add = FALSE, pos = -1, ...) {
  
  ## 4 different types can be used as tab :
  ## distance matrix (dist), contingency table (table), data.frame or matrix
  
  ## evaluation of some parameters
  thecall <- .expand.call(match.call())
  thecall$method <- match.arg(method)
  thecall$symbol <- match.arg(symbol)
  dftab <- eval(thecall$dftab, envir = sys.frame(sys.nframe() + pos))
  if(any(is.na(dftab)))
    stop("NA entries not accepted")
  
  if(inherits(dftab, "dist")) {
    if(missing(labelsx)){
      thecall$labelsx <- labelsx <- NULL
      if(!is.null(attr(dftab, "Labels")))
        if(storeData)
          labelsx <- attr(dftab, "Labels")
        else
          thecall$labelsx <- call("attr", thecall$dftab, "Labels")
    } 
    
    if(missing(labelsy)) {
      thecall$labelsy <- labelsy <- NULL
      if(!is.null(attr(dftab, "Labels")))
        if(storeData)
          labelsy <- attr(dftab, "Labels")
        else
          thecall$labelsy <- call("attr", thecall$dftab, "Labels")
    }
    ## coordsx and coordsy should be identical for dist objects (symmetric)
    thecall$coordsx <- call(":", 1, call("attr", thecall$dftab, "Size"))
    thecall$coordsy <- call(":", call("attr", thecall$dftab, "Size"), 1)
    
  } else { ## data.frame, matrix, table
    if(missing(labelsy)) {
      thecall$labelsy <- labelsy <- NULL
      if(!is.null(rownames(dftab)))
        if(storeData)
          labelsy <- rownames(dftab)
        else
          thecall$labelsy <- call("rownames", thecall$dftab)
    }
    
    if(missing(labelsx)) {
      thecall$labelsx <- labelsx <- NULL
      if(!is.null(colnames(dftab)))
        if(storeData)
          labelsx <- colnames(dftab)
        else
          thecall$labelsx <- call("colnames", thecall$dftab)
    }
  }
  
  
  ## parameters sorted
  sortparameters <- sortparamADEg(...)
  ## creation of the ADEg object
  g.args <- c(sortparameters$g.args, list(breaks = breaks, method = thecall$method, symbol = thecall$symbol, center = thecall$center, col = col, nclass = nclass, centerpar = centerpar))
  if(storeData)
    tmp_data <- list(dftab = dftab, coordsx = coordsx, coordsy = coordsy, labelsx = labelsx, labelsy = labelsy, frame = sys.nframe() + pos, storeData = storeData)
  else
    tmp_data <- list(dftab = thecall$dftab, coordsx = thecall$coordsx, coordsy = thecall$coordsy, labelsx = thecall$labelsx, labelsy = thecall$labelsy, frame = sys.nframe() + pos, storeData = storeData)
  
  if(inherits(dftab, "table")) {
    condres <- pmatch(c("ablineX", "ablineY", "meanX", "meanY"), names(sortparameters$rest))
    if(any(!is.na(condres))) {
      tmplist <- sortparameters$rest[condres[!is.na(condres)]]
      names(tmplist) <- c("ablineX", "ablineY", "meanX", "meanY")[which(!is.na(condres))]
      sortparameters$rest <- sortparameters$rest[-condres[(!is.na(condres))]]
      g.args <- c(g.args, tmplist)
    }
    g.args[c("ablineX", "ablineY", "meanX", "meanY")[which(is.na(condres))]] <- FALSE
    object <- new(Class = "T.cont", data = tmp_data, adeg.par = sortparameters$adepar, trellis.par = sortparameters$trellis, g.args = g.args, Call = match.call())
  } else
    object <- new(Class = "T.value", data = tmp_data, adeg.par = sortparameters$adepar, trellis.par = sortparameters$trellis, g.args = g.args, Call = match.call())
  
  if(length(sortparameters$rest))
    warning(c("Unused parameters: ", paste(unique(names(sortparameters$rest)), " ", sep = "")), call. = FALSE)
  
  ## preparation of the graph
  prepare(object)
  setlatticecall(object)
  if(add)
    object <- add.ADEg(object)
  else
    if(plot)
      print(object)
  invisible(object) 
}