R/S2.value.R

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

#########################################################
###                     s.value                        ##
#########################################################

## TO DO: calcul place legend, taille des points
## Remarque ==> pour size, si couleur selon <0 ou >0 il faut s'assurer que 0 ne sera donc pas dans un intervalle? (inclus ex [-1, 1])
setClass(
  Class = "S2.value",
  contains = "ADEg.S2"
)


setMethod(
  f = "initialize",
  signature = "S2.value",
  definition = function(.Object, data = list(dfxy = NULL, z = NULL, xax = 1, yax = 2, frame = 0, storeData = TRUE), ...) {
    .Object <- callNextMethod(.Object, data = data, ...) ## ADEg.S2 initialize
    .Object@data$z <- data$z
    return(.Object)
  })


setMethod(
  f = "prepare",
  signature = "S2.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$storeData)
      z <- object@data$z
    else
      z <- eval(object@data$z, envir = sys.frame(object@data$frame))
    
    if(is.null(object@adeg.par$ppoints$alpha))
      adegtot$ppoints$alpha <- 0.9
    if(is.null(object@adeg.par$ppoints$cex))
      adegtot$ppoints$cex <- 1
    if(is.null(object@adeg.par$porigin$include) & (any(names(object@g.args) %in% c("Sp", "nbobject"))))
      adegtot$porigin$include <- FALSE
    
    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)
    
    ## 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
    }
    
    if(is.null(object@adeg.par$psub$position))
      adegtot$psub$position <- "topleft"
    
    ## setting colors
    if(!is.null(object@g.args$col)) {
      switch(object@g.args$method,
             size = {
               if(length(object@g.args$col) != 2)
                 stop("if method size choosen, col vector should be size 2", call. = FALSE)
               adegtot$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$quanti(n - 1)
      else
        adegtot$ppoints$col <- adegtot$ppalette$quanti(2)
    }
    
    ## object modification before calling inherited method
    object@adeg.par <- adegtot
    callNextMethod() ## prepare graph
    
    ## never optimized labels for s.value
    object@adeg.par$plabels$optim <- FALSE
    
    assign(name_obj, object, envir = parent.frame())
  })


## Draw symbols according to the different methods
setMethod(
  f = "panel",
  signature = "S2.value",
  definition = function(object, x, y) {
    if(object@data$storeData)
      zorig <- object@data$z
    else
      zorig <- eval(object@data$z, envir = sys.frame(object@data$frame))
    
    adeg.panel.values(x = x, y = y, z = zorig, 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$centerpar, center = object@g.args$center)
  })


s.value <- function(dfxy, z, breaks = NULL, xax = 1, yax = 2, method = c("size", "color"), symbol = c("square", "circle", "diamond", "uptriangle", "downtriangle"),
                    col = NULL, nclass = 4, center = 0, centerpar = NULL, facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...) {
  
  ## evaluation of some parameters
  thecall <- .expand.call(match.call())
  thecall$method <- match.arg(method)
  if(thecall$method == "color") {
    if(center != 0 | !is.null(centerpar))
      warning("'center' and 'centerpar' are not used with 'color' method", call. = FALSE)      
    center <- 0
    centerpar <- NULL
  }
  thecall$center <- center
  thecall$centerpar <- centerpar
  
  thecall$symbol <- match.arg(symbol)
  df <- try(as.data.frame(eval(thecall$dfxy, envir = sys.frame(sys.nframe() + pos))), silent = TRUE)
  z <- eval(thecall$z, envir = sys.frame(sys.nframe() + pos))
  if(inherits(df, "try-error") | is.null(thecall$dfxy)) ## non convenient dfxy argument
    stop("non convenient selection for dfxy (can not be converted to dataframe)", call. = FALSE)
  if(NROW(df) != NROW(z))
    stop("dfxy and z should have the same number of rows", call. = FALSE)
  
  ## parameters sorted
  sortparameters <- sortparamADEg(...)
  
  ## facets
  if(!is.null(facets)) {
    if((length(xax) == 1 & length(yax) == 1) & NCOL(z) == 1)
      object <- multi.facets.S2(thecall, sortparameters$adepar, samelimits = sortparameters$g.args$samelimits)
    else 
      stop("Facets are not allowed with multiple xax/yax or multiple z", call. = FALSE)
  }
  
  ## multiple axes
  else if((length(xax) > 1 | length(yax) > 1)) {
    if(NCOL(z) == 1)
      object <- multi.ax.S2(thecall)
    else 
      stop("Multiple xax/yax are not allowed with multiple z", call. = FALSE)
  }
  
  ## multiple z
  else if(NCOL(z) > 1) {
    object <- multi.variables.S2(thecall, "z")
  }
  
  ## simple ADEg graphic
  else {
    if(length(sortparameters$rest))
      warning(c("Unused parameters: ", paste(unique(names(sortparameters$rest)), " ", sep = "")), call. = FALSE)
    
    ## creation of the ADEg object
    g.args <- c(sortparameters$g.args, list(method = thecall$method, symbol = thecall$symbol, center = center, breaks = breaks, col = col,
                                            nclass = nclass, centerpar = centerpar))
    if(storeData)
      tmp_data <- list(dfxy = dfxy, xax = xax, yax = yax, z = z, frame = sys.nframe() + pos, storeData = storeData)
    else
      tmp_data <- list(dfxy = thecall$dfxy, xax = xax, yax = yax, z = thecall$z, frame = sys.nframe() + pos, storeData = storeData)
    object <- new(Class = "S2.value", data = tmp_data, adeg.par = sortparameters$adepar, trellis.par = sortparameters$trellis, g.args = g.args, Call = as.call(thecall))
    
    ## preparation of the graph
    prepare(object)
    setlatticecall(object)
    if(add)
      object <- add.ADEg(object)
  }
  
  if(! add & plot)
    print(object)
  invisible(object)
}