R/ADEgS.R

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

##############################################
##               general class              ##
##############################################

setClass(
    Class = "ADEgS",
    slots = c(
        ADEglist = "list",
        positions = "matrix",
        add = "matrix",  ## n*n, if xij = 1, j superposed to i
        Call = "call"),
    ## slots checking
    validity = function(object) {
        ng <- length(object@ADEglist)
        add <- object@add
        if (ncol(object@positions) != 4)
            stop("wrong positions matrix, only 4 columns expected (x0, y0, x1, y1)")
        if (nrow(object@positions) != ng)
            stop("not enough positions: rows number of the positions matrix should be equal to the number of graphics in the ADEglist")
        ## checking add:
        if ((NROW(add) != NCOL(add)) | (NCOL(add) != ng))
            stop("add matrix dimensions are not equal to the number of graphics in ADEglist")
        if (any(add != 0 & add != 1))
            stop("add matrix can only contain 0/1 values")
        for (i in 1:ng) {
            j <- 1:i
            if (any(add[i, j] != 0))
                stop("upper diagonal matrix expected for add, only 0 are allowed for xij, when j > = i")
        }
        return(TRUE)
    })

##############################################          
##                 initialize               ##
##############################################       

setMethod(
    f = "initialize",
    signature = "ADEgS",
    function(.Object, ADEglist, positions, add, Call) {
        ## add linking
        superpose <- list()
        ng <- length(ADEglist)
        for (i in 1:ng) {
            superpose <- c(superpose, list(which(add[, i] == 1)))  ## where i is superposed to 1
            if (length((superpose[[i]]))) {
                for (j in superpose[[i]]) {
                    add[superpose[[j]], i] <- 1
                    superpose[[i]] <- c(superpose[[i]], superpose[[j]])
                }}}
        .Object@add <- add
        
        ## check names of the list ADEglist
        if (is.null(names(ADEglist)))
            names(ADEglist) <- paste("g", lapply(1:length(ADEglist), function(i) i), sep = "")
        else
            names(ADEglist) <- make.names(names(ADEglist),unique = TRUE)
        
        ## assignation
        .Object@ADEglist <- ADEglist
        .Object@positions <- positions
        .Object@add <- add
        .Object@Call <- Call
        ## checking validations
        validObject(.Object)
        return(.Object)
    })


setClassUnion(name = "ADEgORADEgSORtrellis", members = c("ADEg", "ADEgS", "trellis"))


##############################################          
##      Get elements/information            ##
##############################################

setMethod(
    f = "getcall",
    signature = "ADEgS",
    definition = function(object) {
        return(object@Call)
    })


setMethod(
    f = "getgraphics",
    signature = "ADEgS",
    definition = function(object) {
        return(object@ADEglist)
    })

setMethod(
    f = "getpositions",
    signature = "ADEgS",
    definition = function(object) {	
        return(object@positions)
    })


setMethod(
    f = "length",
    signature = "ADEgS",
    definition = function(x) {
        return(length(x@ADEglist))
    })


setMethod(
    f = "names",
    signature = "ADEgS",
    definition = function(x) {
        return(names(x@ADEglist))
    })


setMethod(
    f = "names<-",
    signature = c("ADEgS", "character"),
    definition = function(x, value) {
        nameobj <- deparse(substitute(x))
        names(x@ADEglist) <- value
        x
    })

##############################################          
##             Extract graphics             ##
##############################################

## [: if drop =TRUE can return a ADEg or a length-1 ADEgS
## else return a ADEgS no manipulation is made on the positions

setMethod(
    f = "[",
    signature = c("ADEgS", "numeric", "missing", "logical"),
    definition = function(x, i, j, drop = TRUE) {
        if (drop && length(i) == 1)
            return(x@ADEglist[[i]])   ## return(adeG)
        else
            return(new(Class = "ADEgS", ADEglist = x@ADEglist[i], positions = x@positions[i, , drop = drop], add = x@add[i, i, drop = drop], Call = match.call()))
    })


setMethod(
    f = "[",
    signature = c("ADEgS", "numeric", "missing", "missing"),
    definition = function(x, i, j, drop) {
        object <- x[i, drop = FALSE]
        object@Call <- match.call()
        return(object)
    })


setMethod(
    f = "$",
    signature = "ADEgS",
    definition = function(x, name) {
        invisible(x@ADEglist[[name]])
    })

setMethod(
    f = "[[",
    signature = c("ADEgS", "numeric", "missing"),
    definition = function(x, i, j, ...) {
        invisible(x@ADEglist[[i]])
    })


setMethod(
    f = "[[",
    signature = c("ADEgS", "character", "missing"),
    definition = function(x, i, j, ...) {
        invisible(x@ADEglist[[i]])
    })

setMethod(
    f = "[[<-",
    signature = c("ADEgS", "numeric", "missing", "ADEg"),
    definition = function(x, i, j, ..., value) {
        x@ADEglist[[i]] <- value
        invisible(x)
    })

setMethod(
    f = "[[<-",
    signature = c("ADEgS", "numeric", "missing", "ADEgS"),
    definition = function(x, i, j, ..., value) {
        x@ADEglist[[i]] <- value
        invisible(x)
    })

##############################################          
##               superposition              ##
##############################################

setMethod(
    f = "superpose",
    signature = c("ADEgS", "ADEgORtrellis", "numeric", "logical"),
    definition = function(g1, g2, which, plot) {
        ## new ADEgS
        ngraph <- length(g1)
        if (which > ngraph)
            stop("Values in 'which' should be lower than the length of g1")
        
        if (!inherits(g1[[which]], "ADEg")) 
            stop("superposition is only available between two ADEg")
        addi <- cbind(rbind(g1@add, rep(0, ngraph)), rep(0, ngraph + 1))
        addi[which, ngraph + 1] <- 1  ## new graph superpose to which
        ADEglist <- g1@ADEglist
        ADEglist[[ngraph + 1]] <- g2
        ADEgS <- new(Class = "ADEgS", ADEglist = ADEglist, positions = rbind(g1@positions, g1@positions[which,]), add = addi, Call = match.call())
        if (plot) 
            print(ADEgS)
        invisible(ADEgS)
    })


setMethod(
    f = "superpose",
    signature = c("ADEgS", "ADEgORtrellis", "numeric", "ANY"),
    definition = function(g1, g2, which, plot) {
        objectnew <- superpose(g1, g2, which = which, plot = FALSE)
        objectnew@Call <- match.call()
        if (plot)
            print(objectnew)
        invisible(objectnew)            
    })


setMethod(
    f = "superpose",
    signature = c("ADEgS", "ADEgORtrellis", "missing", "ANY"),
    definition = function(g1, g2, which, plot) {
        if (!inherits(g1[[length(g1)]], "ADEg"))
            stop("superposition is only available between two ADEg")
        objectnew <- superpose(g1, g2, which = length(g1), plot = FALSE)
        objectnew@Call <- match.call()
        if (plot)
            print(objectnew)
        invisible(objectnew)
    })


setMethod(
    f = "superpose",
    signature = c("ADEgS", "ADEgS", "missing", "ANY"),
    definition = function(g1, g2, which, plot) {
        ## superpose two ADEgS which have the same number of graphics and the same positions 
        if (length(g1) != length(g2))
            stop("The two ADEgS objects should contain the same number of graphics")
        if (!isTRUE(all.equal(g1@positions, g2@positions, check.attributes = FALSE)))
            stop("The two ADEgS objects should have the same 'positions' slot")
        
        f1 <- function(x, y) {
            if (inherits(x, "ADEg")) {
                addi <- matrix(0, 2, 2)
                addi[1,2] <- 1
                thecall <- call("superpose", x@Call, y@Call)
                obj <- new(Class = "ADEgS", ADEglist = list(x, y), positions = matrix(rep(c(0, 1), each = 4), 2, 4), add = addi, Call = thecall)
            } else if (inherits(x, "ADEgS")) {
                addi <- x@add
                ng <- ncol(addi)
                posi <- x@positions
                
                ## check that positions in posi are all equal and one 1 in each column of addi (i.e. graphs are still superposed)
                checkadd <- all(colSums(addi[, -1, drop = FALSE]) > 0) 
                checkpos <- isTRUE(all.equal(matrix(posi[1, ], nrow = nrow(posi), ncol = ncol(posi), byrow = TRUE), posi))
                if (!checkpos | !checkadd)
                    stop("ADEgS object should contain only superposition")
                
                ## superpose
                addi <- rbind(addi, rep(0, ng))
                addi <- cbind(addi, rep(0, ng + 1))
                addi[ng, ng + 1] <- 1
                
                posi <- rbind(posi, posi[1,])
                thecall <- call("superpose", x@Call, y@Call)
                obj <- new(Class = "ADEgS", ADEglist = c(x@ADEglist, list(y)), positions = posi, add = addi, Call = thecall)
            }
            invisible(obj)
        }
        
        res <- lapply(1:length(g1), FUN = function(i) {f1(g1[[i]], g2[[i]])})
        obj <- new(Class = "ADEgS", ADEglist = res, positions = g1@positions, add = g1@add, Call = match.call())
        
        if (plot)
            print(obj)
        invisible(obj)
    })


setMethod(
    f = "+",
    signature = c("ADEgS", "ADEg"),
    definition = function(e1, e2) {
        newobj <- superpose(e1, e2, plot = TRUE)
        newobj@Call <- match.call()
        return(newobj)
    })


setMethod(
    f = "+",
    signature = c("ADEg", "ADEgS"),
    definition = function(e1, e2) {
        newobj <- superpose(e2, e1, plot = TRUE)
        warning("the second graph is below the first one ; the reverse situation is not yet implemented", call. = FALSE)
        newobj@Call <- match.call()
        return(newobj)
    })


setMethod(
    f = "cbindADEg", 
    signature = c("ADEgORADEgSORtrellis", "ADEgORADEgSORtrellis"),
    definition = function(g1, g2, ..., plot = FALSE) {
        if (try(is.list(...), silent = TRUE) == TRUE)
            glist <- as.list(c(g1, g2, ...))
        
        else
            glist <- list(g1, g2, ...)
        
        nbg <- length(glist)
        obj <- ADEgS(adeglist = glist, layout = c(1, nbg), add = matrix(0, ncol = nbg, nrow = nbg), plot = FALSE)
        obj@Call <- match.call()
        
        if (plot)
            print(obj)
        invisible(obj)
    })


setMethod(
    f = "rbindADEg", 
    signature = c("ADEgORADEgSORtrellis", "ADEgORADEgSORtrellis"),
    definition = function(g1, g2, ..., plot = FALSE) {
        if (try(is.list(...), silent = TRUE) == TRUE)
            glist <- as.list(c(g1, g2, ...))
        else
            glist <- list(g1, g2, ...)
        
        nbg <- length(glist)
        obj <- ADEgS(adeglist = glist, layout = c(nbg, 1), add = matrix(0, ncol = nbg, nrow = nbg), plot = FALSE)
        obj@Call <- match.call()
        
        if (plot)
            print(obj)
        invisible(obj)
    })


##############################################        
##                   insertion              ##
##############################################

setMethod(
    f = "insert", 
    signature = c("ADEgS", "missing"),
    definition = function(graphics, oldgraphics, posi, ratio, inset, plot, which, dispatch) {
        positions <- .getposition(posi, w = ratio, h = ratio) + inset
        currentgraphic <- get("currentadeg", envir = .ADEgEnv)
        if (!(length(currentgraphic)))
            stop("no existing graphics")
        else
            newADEgS <- insert(graphics = graphics, oldgraphics = currentgraphic, posi = posi, ratio = ratio, inset = inset, plot = plot, which = which, dispatch = dispatch)
        
        if (plot)
            print(newADEgS[length(newADEgS)], newpage = FALSE)
        assign("currentadeg", newADEgS, envir = .ADEgEnv)
        invisible(newADEgS)
    })


setMethod(
    f = "insert", 
    signature = c("ADEgS", "ADEg"),
    definition = function(graphics, oldgraphics, posi, ratio, inset, plot) {
        positions <- .getposition(posi, w = ratio, h = ratio) + inset
        thecall <- call("insert", graphics@Call, oldgraphics@Call)
        newADEgS <- new(Class = "ADEgS", ADEglist = list(oldgraphics, graphics), positions = rbind(c(0, 0, 1, 1), positions), add = matrix(0, ncol = 2, nrow = 2), thecall)
        if (plot)      
            print(newADEgS)
        
        assign("currentadeg", newADEgS, envir = .ADEgEnv)
        invisible(newADEgS)
    })


setMethod(
    f = "insert", 
    signature = c("ADEgORtrellis", "ADEgS"),
    definition = function(graphics, oldgraphics, posi, ratio, inset, plot, which) {
        thecall <- call("insert", graphics@Call, oldgraphics@Call)
        if (missing(which)) {
            positions <- .getposition(posi, w = ratio, h = ratio) + inset
            newADEgS <- new(Class = "ADEgS", ADEglist = c(oldgraphics@ADEglist, list(graphics)), positions = rbind(oldgraphics@positions, positions), add = rbind(cbind(oldgraphics@add, rep(0, length.out = nrow(oldgraphics@add))), rep(0, length.out = ncol(oldgraphics@add) + 1)), Call = thecall)
        } else {
            l <- sapply(1:length(oldgraphics), FUN = function(i) {if (i %in% which) {insert(graphics, oldgraphics@ADEglist[[i]], posi = posi, ratio = ratio, inset = inset, plot = FALSE)} else oldgraphics@ADEglist[[i]]})
            newADEgS <- new(Class = "ADEgS", ADEglist = l, positions = oldgraphics@positions, add = oldgraphics@add, Call = thecall)
        }
        
        if (plot)
            print(newADEgS)
        assign("currentadeg", newADEgS, envir = .ADEgEnv)
        invisible(newADEgS)
    })


setMethod(
    f = "insert", 
    signature = c("ADEgS", "ADEgS"),
    definition = function(graphics, oldgraphics, posi, ratio, inset, plot, which, dispatch) {
        thecall <- call("insert", graphics@Call, oldgraphics@Call)
        if (!dispatch){
            if (missing(which)) {
                positions <- .getposition(posi, w = ratio, h = ratio) + inset
                newADEgS <- new(Class = "ADEgS", ADEglist = c(oldgraphics@ADEglist, list(graphics)), positions = rbind(oldgraphics@positions, positions), add = rbind(cbind(oldgraphics@add, rep(0, length.out = nrow(oldgraphics@add))), rep(0, length.out = ncol(oldgraphics@add) + 1)), Call = thecall)
            } else {
                l <- sapply(1:length(oldgraphics), FUN = function(i) {if (i %in% which) {insert(graphics, oldgraphics@ADEglist[[i]], posi = posi, ratio = ratio, inset = inset, plot = FALSE)} else oldgraphics@ADEglist[[i]]})
                newADEgS <- new(Class = "ADEgS", ADEglist = l, positions = oldgraphics@positions, add = oldgraphics@add, Call = thecall)
            }
        } else {
            if (length(graphics) != length(oldgraphics))
                stop("dispatch option is not allowed with ADEgS object of different length")
            else {
                l <- sapply(1:length(oldgraphics), FUN = function(i) {insert(graphics@ADEglist[[i]], oldgraphics@ADEglist[[i]], posi = posi, ratio = ratio, inset = inset, plot = FALSE)})
                newADEgS <- new(Class = "ADEgS", ADEglist = l, positions = oldgraphics@positions, add = oldgraphics@add, Call = thecall)
            }
        }
        
        if (plot)
            print(newADEgS)
        assign("currentadeg", newADEgS, envir = .ADEgEnv)
        invisible(newADEgS)
    })

##############################################          
##                  Update                  ##
##############################################

## update the modified parameters
setMethod(
    f = "update",
    signature = "ADEgS",
    definition = function(object, ..., plot = TRUE) {
        nameobj <- deparse(substitute(object, env = parent.frame()))
        ## object is in parent.frame() because 'update' method pattern is different with 'update' generic method pattern
        ## see https://stat.ethz.ch/pipermail/r-help/2008-January/152296.html
        
        slots <- list()
        slots$names <- names(object)
        slots$positions <- object@positions
        
        ## extract specific slots used in function call
        pattern <- c("names", "positions")
        lpattern <- as.list(rep("", length(pattern)))
        names(lpattern) <- pattern
        
        ## sort parameters
        sep <- separation(..., pattern = lpattern)
        slots <- modifyList(slots, sep[[1]], keep.null = TRUE)
        sep[[2]] <- sortparamADEgS(sep[[2]], graphsnames = slots$names)
        
        ADEglist <- sapply(1:length(object@ADEglist), FUN = function(x) {if (inherits(object@ADEglist[[x]], "ADEg") | inherits(object@ADEglist[[x]], "ADEgS")) update(object@ADEglist[[x]], plot = FALSE, sep[[2]][[x]]) else do.call("update", c(list(object = object@ADEglist[[x]]), sep[[2]][[x]]))})
        object <- new("ADEgS", ADEglist = ADEglist, positions = slots$positions, add = object@add, Call = match.call())
        names(object) <- slots$names
        
        if (plot)
            print(object)
        assign(nameobj, object, envir = parent.frame(n = 2))
        ## see also https://stat.ethz.ch/pipermail/r-help/2008-January/152296.html
        
        assign("currentadeg", object, envir = .ADEgEnv)
    })

##############################################          
##                   Display                ##
##############################################

setMethod(
    f = "show",
    signature = "ADEgS",
    definition = function(object) {
        print(object)
    })


setMethod(
    f = "plot",
    signature = c("ADEgS", "ANY"),
    definition = function(x, y) {
        print(x)
    })


setMethod(
    f = "print",
    signature = "ADEgS",
    definition = function(x, closeViewport = TRUE, square = NULL) {
        oldtextcex <- trellis.par.get("fontsize")$text
        oldpointcex <- trellis.par.get("fontsize")$points
        oldmarginH <- trellis.par.get("layout.heights")
        oldmarginW <- trellis.par.get("layout.widths")
        
        trellis.par.set(layout.heights = list(top.padding = .2 + oldmarginH$top.padding, bottom.padding = .2 + oldmarginH$bottom.padding), layout.widths = list(left.padding = .2 + oldmarginW$left.padding, right.padding = .2 + oldmarginW$right.padding))
        on.exit(trellis.par.set(list("fontsize" = list("text" = oldtextcex, "points" = oldpointcex), "layout.widths" = list("left.padding" = oldmarginW$left.padding, "right.padding" = oldmarginW$right.padding), "layout.heights" = list("top.padding" = oldmarginH$top.padding, "bottom.padding" = oldmarginH$bottom.padding))))
        
        gettextsize <- function(widG, heigG) {
            ## Adjust text size to viewport size
            if (widG < 1 / 2 || heigG < 1 / 2)
                return(0.66 / 1.25)
            if (widG == 1 / 2 && heigG == 1 / 2)
                return(0.83 / 1.25)
            if (widG == 1 && heigG == 1)
                return(1)
            else return(1 / 1.25)              
        }
        
        getxscale <- function(object) {
            ## Obtain limits for x
            res <- c(0, 1)
            if (inherits(object, "ADEg"))
                object <- gettrellis(object)
            if (inherits(object, "trellis")) {
                if (is.numeric(object$x.limits))
                    res <- object$x.limits
            } 
            return(res)
        }
        
        getyscale <- function(object) {
            ## Obtain limits for y
            res <- c(0, 1)
            if (inherits(object, "ADEg"))
                object <- gettrellis(object)
            if (inherits(object, "trellis")) {
                if (is.numeric(object$y.limits))
                    res <- object$y.limits
            } 
            return(res)
        }
        
        printADEGs <- function(adegobject, closeViewport, square) {
            if (closeViewport)
                grid.newpage()
            
            positions <- adegobject@positions
            listG <- adegobject@ADEglist
            
            ## create the list of viewport and push it
            unit.vpL <- "npc"
            if (isTRUE(square))
                unit.vpL <- "snpc"
            
            vpL <- do.call("vpList", lapply(1:length(listG), function(i) do.call("viewport", args = list(x = positions[i, 1], y = positions[i, 2], width = positions[i, 3] - positions[i, 1], height = positions[i, 4] - positions[i, 2], just = c(0, 0), name = names(listG)[i], xscale = getxscale(listG[[i]]), yscale = getyscale(listG[[i]]), default.units = unit.vpL))))
            pushViewport(vpL)
            
            upViewport(0)
            width.root <- convertWidth(unit(1, unit.vpL), "inches", valueOnly = TRUE)
            height.root <- convertHeight(unit(1, unit.vpL), "inches", valueOnly = TRUE)
            
            for (i in 1:length(listG)) {
                object <- listG[[i]]
                seekViewport(names(listG)[i])
                
                if (inherits(object, "ADEg") | inherits(object, "trellis")) {
                    if (inherits(object, "ADEg"))
                        trobject <- gettrellis(object)
                    else
                        trobject <- object
                    
                    square.i <- ifelse(is.null(square), !trobject$aspect.fill, square)
                    unit.vpi <- "npc"
                    if (isTRUE(square.i))
                        unit.vpi <- "snpc"
                    
                    vp <- viewport(x = 0, y = 0, width = 1, height = 1, just = c(0, 0), name = "current", xscale = getxscale(listG[[i]]), yscale = getyscale(listG[[i]]), default.units = unit.vpi)
                    pushViewport(vp)
                    
                    width.current <- convertWidth(unit(1, unit.vpi), "inches", valueOnly = TRUE)
                    height.current <- convertHeight(unit(1, unit.vpi), "inches", valueOnly = TRUE)
                    ratio.width <- width.current / width.root
                    ratio.height <- height.current / height.root
                    
                    cst <- gettextsize(ratio.width, ratio.height)
                    sup <- adegobject@add[, i]
                    trellis.par.set(list("fontsize" = list("text" = oldtextcex * cst, "points" = oldpointcex * cst)))
                    if (any(sup == 1))
                        printSuperpose(g1 = object, refg = listG[[which(adegobject@add[, i] == 1)[1]]])
                    else
                        print(object, newpage = FALSE)
                    
                    popViewport()
                    
                } else if (inherits(object, "ADEgS")) {
                    names(object) <- paste(names(listG)[i], names(object), sep = ".")
                    printADEGs(object, closeViewport = FALSE, square = square)
                } else {
                    stop(paste("Not implemented for class:", class(object), sep = " "))
                }
                popViewport()
            }
        }
        
        printADEGs(x, closeViewport = closeViewport, square = square)
        assign("currentadeg", x, envir = .ADEgEnv)
    })


##############################################          
##                   Creation               ##
##############################################

ADEgS <- function(adeglist, positions, layout, add = NULL, plot = TRUE) {
    
    m <- matrix(0, length(adeglist), length(adeglist))
    
    if (missing(layout) & (is.null(add) | identical(add, m)) & missing(positions))
        layout <- .n2mfrow(length(adeglist))
    
    if (missing(positions) & !missing(layout)) {
        if (is.list(layout)) ## in layout: width and heights informations, layout is a list
            positions <- do.call("layout2position", layout)
        else
            positions <- layout2position(layout, ng = length(adeglist))
    }
    
    if (missing(positions)) 
        positions <- matrix(rep(c(0, 0, 1, 1), length.out = length(adeglist) * 4), byrow = TRUE, ncol = 4)
    
    if (is.null(add))
        add <- m
    
    ADEgObject <- new(Class = "ADEgS", ADEglist = adeglist, positions = positions, add = add, Call = match.call())
    if (plot)
        print(ADEgObject)
    invisible(ADEgObject)
}