R/plot.argument.handlers.R

In loa: Lattice Options and Add-Ins

#in development code
#[TBC - NUMBER] functions 


#scalesHandler
#cexHandler
#colHandler
#colRegionsHandler
#pchHandler
#zHandler

#[in-development]
#parHandler

#to think about



#TO DO urgent
###############
#in getPlotArgs
#URGENT quickfix in place 
#needs a rewrite
#also think about order of formals



#to do
###############
#think about hardcoded defaults
#on col and cex


#to think about
###############
#might be better replacing 
#zhandler with listExpand
#


#NOTE: much borrowed from lattice 


######################
######################
##scalesHandler
######################
######################

#this need tidying...

scalesHandler <- function(...){
    ans <- listLoad(..., load="scales")

#this needs to loose the arguments
#scales$x...
#scales$y... 
#after they have been used...

    temp <- do.call(listLoad, listUpdate(ans$scales, list(load="x")))
    ans$scales$x <- temp$x
    temp <- do.call(listLoad, listUpdate(ans$scales, list(load="y")))
    ans$scales$y <- temp$y
   ans
}














#####################
#####################
##cexHandler
#####################
#####################

#local function to handler cex
#when supplying a z argument to xyplot
#[in development]

cexHandler <- function(z = NULL, cex = NULL, 
         cex.range = NULL, expand.outputs = TRUE, 
         ref = NULL, ..., zlim = NULL){

    #if cex there use it
    if(!is.null(cex))  
        return(zHandler(cex, expand.outputs, ref))

    if(is.null(cex.range))
        cex.range <- TRUE
    
    cex <- z
        
    #cex.range setup
    if(is.logical(cex.range) && cex.range)
        cex.range <- c(0.75, 3)
    if(is.numeric(cex.range)){
        temp <- range(cex.range, na.rm = TRUE, finite = TRUE)
        cex.range <- if(length(na.omit(temp)) < 2)
                         FALSE else temp
    }

    #cex default 
    cex.ref <- min(cex.range, na.rm=TRUE) + (0.2 * (max(cex.range, na.rm=TRUE)- min(cex.range, na.rm=TRUE)))



    if(is.null(cex) || length(na.omit(cex))<1){
        cex <- if(is.numeric(cex.range)) cex.ref else 1
    } else {
        cex <- as.numeric(cex)

        if(!is.null(zlim)){
              temp <- range(as.numeric(zlim), na.rm = TRUE, finite = TRUE)
              cex[cex < min(zlim, na.rm=TRUE) | cex > max(zlim, na.rm=TRUE)] <- NA
        } else {
              temp <- range(cex, na.rm = TRUE, finite = TRUE)
        }

        #temp <- range(cex, na.rm = TRUE, finite = TRUE)


        my.range <- if(length(na.omit(temp)) < 2)
                        FALSE else temp
        if(is.numeric(cex.range)){
            if(my.range[1] == my.range[2]){
                cex[cex == my.range[1]] <- cex.ref
            } else {
                temp <- (cex.range[2]-cex.range[1]) / (my.range[2]-my.range[1])
                cex <- cex.range[1] + (cex - my.range[1]) * temp
            }
        }
    }
 
    #return cex 
    #scaled by ref if requested
################
#testing
    cex[is.na(cex)] <- 0
################
    return(zHandler(cex, expand.outputs, ref))

}



#####################
#####################
##colHandler
#####################
#####################

#local function to handler col and colorkey
#when supplying a z argument to xyplot
#[in development]


#rescue group

colHandler <- function (z = NULL, col = NULL, region = NULL, colorkey = FALSE, 
    legend = NULL, pretty = FALSE, at = NULL, cuts = 20, col.regions = NULL, 
    alpha.regions = NULL, expand.outputs = TRUE, ref = NULL, 
    ..., zlim = NULL, output = "col") 
{
    extra.args <- list(...)

    if ("scheme" %in% names(extra.args) & !"par.settings" %in% 
        names(extra.args)) 
        extra.args$par.settings <- do.call(parHandler, extra.args)
    if (is.null(col.regions) & !is.null(extra.args$par.settings)) 
        col.regions <- extra.args$par.settings$regions$col
############
#job 1 
#new lines 
#could merge this, one above and one below
    if(is.null(col.regions))
         col.regions <- lattice::trellis.par.get("regions")$col
###############
    if (!is.null(col.regions) && length(col.regions) < 100) {
        if (length(col.regions) == 1) 
            col.regions <- RColorBrewer::brewer.pal(9, col.regions)
################
#above creates issue for some brewer terms...
#only have 8 terms...
        col.regions <- grDevices::colorRampPalette(col.regions)(100)
    }
    if (length(z) < 1) 
        z <- NULL
    if (is.null(z) & is.null(col)) {

###################
#why is this replicated?
        if (is.null(col.regions)) 
            regions <- FALSE
        if (is.null(col.regions)) 
            regions <- FALSE
#################
#testing new default col for z=NULL...
#this might not be quite right      
#following col.regions in panel

#        col <- if(is.null(col.regions)) trellis.par.get("dot.symbol")$col else
#                   colHandler(1, col.regions=col.regions)

#using scheme
        col <- lattice::trellis.par.get("dot.symbol")$col

    }
    if (is.null(col)) {
        if (!is.numeric(z)) {
            z <- as.factor(z)
            zlim <- z
        }
        else {
            if (!is.null(zlim)) {
                z[z < min(zlim, na.rm = TRUE) | z > max(zlim, 
                  na.rm = TRUE)] <- NA
            }
            else {
                zlim <- range(z, finite = TRUE)
            }
        }
        zrng <- range(as.numeric(zlim), finite = TRUE)
        if (length(unique(zrng)) < 2) 
            zrng <- lattice.extend.limits(zrng)
        if (is.null(at)) 
            at <- if (pretty) 
                pretty(zrng, cuts)
            else seq(zrng[1], zrng[2], length.out = cuts + 2)

###############
#cannot be post job 1
#
#        if (is.null(col.regions)) {
#            
#            col <- level.colors(z, at)
#            col.regions <- colorRampPalette(level.colors(at, 
#                at))(100)
#        }
#        else 
       col <- lattice::level.colors(as.numeric(z), at, col.regions)
    }
    else {
        z <- if (is.numeric(col)) 
            col
        else as.factor(col)
        zrng <- range(as.numeric(z), finite = TRUE)
        if (length(unique(zrng)) < 2) 
            zrng <- lattice.extend.limits(zrng)
        if (is.null(at)) 
            at <- if (pretty) 
                pretty(zrng, cuts)
            else seq(zrng[1], zrng[2], length.out = cuts + 2)
    }
    if (is.null(col.regions)) {
        temp <- if (is.numeric(col)) 
            sort(col)
        else col
        temp <- unique(temp)
        temp <- if (length(temp) == 1) 
            c(temp, temp)
        else temp
#################
#job 1
#changed 100 -> length(col.regions)
#
        col.regions <- grDevices::colorRampPalette(lattice::level.colors(at, at, 
                grDevices::colorRampPalette(temp)(length(col.regions))))(length(col.regions))
#################
    }
    if (is.null(alpha.regions)) 
        alpha.regions <- 1
    if (is.logical(alpha.regions) && alpha.regions) 
        alpha.regions <- 0.5
    if (is.numeric(alpha.regions)) {
        if (any(alpha.regions < 0) | any(alpha.regions > 1)) {
            warning(paste("could sensibly apply requested 'alpha.regions'", 
                "\n\t[Suggest numeric in range 0 to 1]", "\n\t[resetting out-of-range value(s) to 0 or 1]", 
                sep = ""), call. = FALSE)
            alpha.regions[alpha.regions > 1] <- 1
            alpha.regions[alpha.regions < 0] <- 0
        }
        col <- col2rgb(col)
        col <- grDevices::rgb(col[1, ], col[2, ], col[3, ], alpha = alpha.regions * 
            255, maxColorValue = 255)
    }
    if (length(unique(col)) > 1) {
        if (is.null(region)) 
            region <- TRUE
        if (is.null(colorkey)) 
            colorkey <- TRUE
    }
    if (is.logical(colorkey)) {
        if (colorkey) {
            colorkey <- list(at = at, space = "right")
            if (!is.null(col.regions)) 
                colorkey$col <- col.regions
            if (!is.null(alpha.regions)) 
                colorkey$alpha <- alpha.regions
        }
        else colorkey <- NULL
    }
    else if (is.list(colorkey)) {
        tmp <- list(space = if (any(c("x", "y", "corner") %in% 
            names(colorkey))) "inside" else "right", at = at)
        if (!is.null(col.regions)) 
            tmp$col <- col.regions
        if (!is.null(alpha.regions)) 
            tmp$alpha <- alpha.regions
        colorkey <- listUpdate(tmp, colorkey)
    }
    else {
        if (!is.null(colorkey)) {
            warning("unexpected colorkey ignored.", call. = FALSE)
            colorkey <- NULL
        }
    }
    if (!is.null(colorkey)) {
        colorkey <- list(right = list(fun = lattice::draw.colorkey, 
                                      args = list(key = lattice::draw.colorkey), 
            draw = FALSE))
        if ("space" %in% names(colorkey$right$args$key)) 
            names(colorkey)[[1]] <- colorkey$right$args$key$space
    }
    if (is.null(legend)) 
        legend <- colorkey
    if (any(is.na(z))) 
        col[is.na(z)] <- "#FFFFFF00"
    col <- zHandler(col, expand.outputs, ref)
    z <- zHandler(z, expand.outputs, ref)
    if (output == "col") 
        return(col)
    list(z = z, col = col, legend = legend, at = at, col.regions = col.regions, 
        alpha.regions = alpha.regions)
}


old.colHandler <- function(z = NULL, col = NULL, 
         region = NULL, colorkey = FALSE, legend = NULL,
         pretty = FALSE, at = NULL, cuts = 20,
         col.regions = NULL, alpha.regions = NULL,
         expand.outputs = TRUE, ref = NULL, 
         ..., zlim = NULL, output="col"){


    #temp update test
    extra.args <- list(...)

###############
#test
    #cuts <- length(z)
###############

    #scheme check
    if("scheme" %in% names(extra.args) & !"par.settings" %in% names(extra.args))
        extra.args$par.settings <- do.call(parHandler, extra.args)


    #check par.settings
#could refer these to extra.args not list(...)

#    if(is.null(col.regions) & !is.null(list(...)$par.settings))
#        col.regions <- list(...)$par.settings$regions$col


    if(is.null(col.regions) & !is.null(extra.args$par.settings))
        col.regions <- extra.args$par.settings$regions$col


    #if col.regions supplied
    if(!is.null(col.regions) && length(col.regions) < 100){
        if(length(col.regions)==1)
            col.regions <- RColorBrewer::brewer.pal(9, col.regions)
         col.regions <- grDevices::colorRampPalette(col.regions)(100)
   }

   #don't assum col.regions is 100 long...
#job 27, added this line
   col.regions.len <- length(col.regions)
#job 28 


   #if both z and col present
   #ignore z when coloring data
#   if(!is.null(z) & !is.null(col)){

#silence this warning
#properly
#       warning("z and col both given, z ignored when coloring data.", call. = FALSE)
#   }

   if(length(z)<1) z <- NULL

   #if neither z nor col available
   #create defaults
   if(is.null(z) & is.null(col)){
        if(is.null(col.regions))
            regions <- FALSE
        if(is.null(col.regions))
            regions <- FALSE
        col <- lattice::trellis.par.get("dot.symbol")$col
   } 

   #z handle if not col
   #else col handle
   if(is.null(col)){
        #just z given
        if(!is.numeric(z)){
            z <- as.factor(z)
            zlim <- z
        } else {
            if(!is.null(zlim)){
                z[z < min(zlim, na.rm=TRUE) | z > max(zlim, na.rm=TRUE)] <- NA
            } else {
                zlim <- range(z, finite=TRUE)
            }
        }
#test fix
#        zrng <- lattice.extend.limits(range(as.numeric(zlim), finite = TRUE))
        zrng <- range(as.numeric(zlim), finite = TRUE)
        if(length(unique(zrng))<2) zrng <- lattice.extend.limits(zrng) 
        if(is.null(at)) 
            at <- if(pretty) 
                      pretty(zrng, cuts) else 
                          seq(zrng[1], zrng[2], length.out = cuts + 2)   
        if(is.null(col.regions)){


#job 27b
#replace below col <- with following one...
            col <- lattice::level.colors(z, at)
#            col <- colorRampPalette(level.colors(1:100, 1:100))(length(z))

#job 27
#100 -> col.regions.len

            col.regions <- grDevices::colorRampPalette(level.colors(at, at))(col.regions.len)
        } else col <- lattice::level.colors(z, at, grDevices::colorRampPalette(col.regions)(length(z)))
#job 27
#col.regions <- colorRampPalette(col.regions)(length(z))

    } else {
        #all other cases use
        #using col
        z <- if(is.numeric(col)) col else as.factor(col)
#test fix
#        zrng <- lattice.extend.limits(range(as.numeric(z), finite = TRUE))
        zrng <- range(as.numeric(z), finite = TRUE)
        if(length(unique(zrng))<2) zrng <- lattice.extend.limits(zrng) 

        if(is.null(at)) 
            at <- if(pretty) 
                     pretty(zrng, cuts) else 
                          seq(zrng[1], zrng[2], length.out = cuts + 2)   
   }

   #creat col.regions if still missing
   if(is.null(col.regions)){
       temp <- if(is.numeric(col)) sort(col) else col
       temp <- unique(temp)
       temp <- if(length(temp) == 1) c(temp, temp) else temp 

#job 27
#100 -> col.regions.len

       col.regions <- grDevices::colorRampPalette(lattice::level.colors(at, at, 
                        grDevices::colorRampPalette(temp)(col.regions.len)))(col.regions.len)
   }                       

   #handle alpha
   if(is.null(alpha.regions))
        alpha.regions <- 1

   if(is.logical(alpha.regions) && alpha.regions)
        alpha.regions <- 0.5
   
   if(is.numeric(alpha.regions)){
       if(any(alpha.regions < 0) | any(alpha.regions > 1)){
           warning(paste("could sensibly apply requested 'alpha.regions'",
                         "\n\t[Suggest numeric in range 0 to 1]", 
                         "\n\t[resetting out-of-range value(s) to 0 or 1]",
                    sep=""), call.=FALSE)
            alpha.regions[alpha.regions > 1] <- 1
            alpha.regions[alpha.regions < 0] <- 0
        }
        col <- col2rgb(col)
        col <- rgb(col[1,], col[2,], col[3,], 
                      alpha = alpha.regions * 255, maxColorValue = 255)
    }    

    #show regions,colorkey if
    #if a col range to work with and either is NULL 
    if(length(unique(col))>1){
        if(is.null(region))
            region <- TRUE
        if(is.null(colorkey))
            colorkey <- TRUE 
    }

    #set up colorkey

#could move defaults out into call?

    if (is.logical(colorkey)) {
        if (colorkey) {
            colorkey <- list(at = at, space = "right")
            if (!is.null(col.regions)) 
                colorkey$col <- col.regions
            if (!is.null(alpha.regions)) 
                colorkey$alpha <- alpha.regions
        }
        else colorkey <- NULL
    } else if (is.list(colorkey)) {
            tmp <- list(space = if (any(c("x", "y", "corner") %in% 
                names(colorkey))) "inside" else "right", at = at)
            if (!is.null(col.regions)) 
                tmp$col <- col.regions
            if (!is.null(alpha.regions)) 
                tmp$alpha <- alpha.regions
            colorkey <- listUpdate(tmp, colorkey)
    } else {
         if(!is.null(colorkey)){
             warning("unexpected colorkey ignored.", call. = FALSE)
             colorkey <- NULL
         }
    }

    #structure like legend
    if(!is.null(colorkey)){
        colorkey <- list(right = list(fun = draw.colorkey,
                         args = list(key = colorkey),
                         draw =FALSE))
       if("space" %in% names(colorkey$right$args$key))    
           names(colorkey)[[1]] <- colorkey$right$args$key$space
    }

    #legend update if not preset
    if(is.null(legend))
          legend <- colorkey

#temp testing 
#na handled as transparent
    if(any(is.na(z)))
        col[is.na(z)] <- "#FFFFFF00"

    #expand z,col if requests and 
    #ref to scale by...
    col <- zHandler(col, expand.outputs, ref)
    z <- zHandler(z, expand.outputs, ref)

#print(col)

    #return relevant settings
    if(output=="col") return(col)
    list(z = z, col = col, 
         legend = legend, at = at, 
         col.regions = col.regions, 
         alpha.regions = alpha.regions)

}









#####################
#####################
##colRegionsHandler
#####################
#####################

#local function to handler col.regions 
#[in development]

colRegionsHandler <- function(...){

#to think about
############################
#might want to refine this?

   extra.args <- list(...)

   if(!"col.regions" %in% names(extra.args))
       return(NULL)

   if("isolate.col.regions" %in% names(extra.args) && extra.args$isolate.col.regions)
       extra.args$col <- NULL

   extra.args$at <- NULL
#   extra.args <- listUpdate(extra.args, list(z=1:100, zlim=c(1,100), output="col")) 
#   do.call(colHandler, extra.args)    
   
   do.call(colHandler, listUpdate(extra.args, 
                                  list(z=1:100, zlim=c(1,100), cuts=99, ref=1:100)))


}








####################
####################
##pchHandler
####################
####################


pchHandler <- function(z = NULL, pch = NULL, 
         pch.order = NULL, expand.outputs = TRUE, 
         ref = NULL, ..., zlim = NULL){

    ##pch handler v0.1

#TO DO
#######################
#zlim handling to add
#######################
#check factor use elsewhere
#NAs in data may be issue
#######################
#

    #if pch there use it
    if(!is.null(pch))  
        return(zHandler(pch, expand.outputs, ref))

    if(is.null(pch.order))
        pch.order <- c(19, 18:15, 21:25, 1:14)
    
    pch <- if(is.null(z))
               pch.order[1] else {
                   temp <- factor(z, exclude=NULL)
                   levels(temp) <- rep(1:length(pch.order), length.out = length(levels(temp)))
                   pch.order[as.numeric(as.character(temp))]
               }

    zHandler(pch, expand.outputs, ref)
}















#####################
#####################
##zHandler
#####################
#####################

#local function to handler simple cases
#expand to ref length
#[in development]

zHandler <- function(z = NULL, expand.outputs = TRUE, 
          ref = NULL, ...){
                
    if(is.null(z)) return(z)
                      
    if(is.null(ref) | !expand.outputs) return(z)
    if(length(z) < length(ref))
        rep(z, ceiling(length(ref)/length(z)))[1:length(ref)] else 
            z[1:length(ref)]
}




#######################
######################
##lattice.extend.limits
######################
#######################


lattice.extend.limits <- function (lim, length = 1, axs = "r", prop = if (axs == "i") 0 else lattice.getOption("axis.padding")$numeric) 
{
    if (all(is.na(lim))) 
        NA_real_
    else if (is.character(lim)) {
        c(1, length(lim)) + c(-1, 1) * if (axs == "i") 
            0.5
        else lattice::lattice.getOption("axis.padding")$factor
    }
    else if (length(lim) == 2) {
        if (lim[1] > lim[2]) {
            ccall <- match.call()
            ccall$lim <- rev(lim)
            ans <- eval.parent(ccall)
            return(rev(ans))
        }
        if (!missing(length) && !missing(prop)) 
            stop("'length' and 'prop' cannot both be specified")
        if (length <= 0) 
            stop("'length' must be positive")
        if (!missing(length)) {
            prop <- (as.numeric(length) - as.numeric(diff(lim)))/(2 * 
                as.numeric(diff(lim)))
        }
        if (lim[1] == lim[2]) 
            lim + 0.5 * c(-length, length)
        else {
            d <- diff(as.numeric(lim))
            lim + prop * d * c(-1, 1)
        }
    }
    else {
        print(lim)
        stop("improper length of 'lim'")
    }
}