###########################################################
## s1d.boxplot ##
###########################################################
setClass(
Class = "S1.boxplot",
contains = "ADEg.S1"
)
setMethod(
f = "initialize",
signature = "S1.boxplot",
definition = function(.Object, data = list(score = NULL, fac = NULL, at = NULL, frame = 0, storeData = TRUE), ...) {
.Object <- callNextMethod(.Object, data = data, ...) ## ADEg.S1 initialize
.Object@data$fac <- data$fac
return(.Object)
})
setMethod(
f = "prepare",
signature = "S1.boxplot",
definition = function(object) {
name_obj <- deparse(substitute(object))
if(object@data$storeData)
fac <- as.factor(object@data$fac)
else
fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
## pre-management of graphics parameters
oldparamadeg <- adegpar()
on.exit(adegpar(oldparamadeg))
adegtot <- adegpar(object@adeg.par)
## change default for some parameters
if(adegtot$p1d$horizontal & is.null(object@adeg.par$plabels$srt))
adegtot$plabels$srt <- 0
else if(!adegtot$p1d$horizontal & is.null(object@adeg.par$plabels$srt))
adegtot$plabels$srt <- 90
## setting colors
paramsToColor <- list(ppoints = list(col = object@adeg.par$ppoints$col, fill = object@adeg.par$ppoints$fill),
plabels = list(col = object@adeg.par$plabels$col, boxes = list(border = object@adeg.par$plabels$boxes$border)),
plines = list(col = object@adeg.par$plines$col),
ppolygons = list(border = object@adeg.par$ppolygons$border, col = object@adeg.par$ppolygons$col))
if(!(is.null(object@g.args$col) || (is.logical(object@g.args$col) && !object@g.args$col)))
adegtot <- modifyList(adegtot, col2adepar(ccol = object@g.args$col, pparamsToColor = paramsToColor, nnlev = nlevels(fac)))
## object modification before calling inherited method
object@adeg.par <- adegtot
callNextMethod() ## prepare graph
assign(name_obj, object, envir = parent.frame())
})
setMethod(
f = "panel",
signature = "S1.boxplot",
definition = function(object, x, y) {
if(object@data$storeData) {
fac <- object@data$fac
at <- object@data$at
} else {
fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
at <- eval(object@data$at, envir = sys.frame(object@data$frame))
}
fac <- as.factor(fac)
nlev <- nlevels(fac)
labels <- levels(fac)
lims <- current.panel.limits(unit = "native")
pscore <- object@adeg.par$p1d
plabels <- object@adeg.par$plabels
## repeat graphical parameters (one for each level)
ppoints <- lapply(object@adeg.par$ppoints, FUN = function(x) x <- rep(x, length.out = nlev))
ppoints <- lapply(ppoints, FUN = function(x) x <- x[1:nlev])
plines <- lapply(object@adeg.par$plines, FUN = function(x) x <- rep(x, length.out = nlev))
plines <- lapply(plines, FUN = function(x) x <- x[1:nlev])
ppolygons <- lapply(object@adeg.par$ppolygons, FUN = function(x) x <- rep(x, length.out = nlev))
ppolygons <- lapply(ppolygons, FUN = function(x) x <- x[1:nlev])
## manage trellis parameters
oldcolsymbol <- trellis.par.get("plot.symbol")$col
oldcolumbrella <- trellis.par.get("box.umbrella")$col
oldcolrectangle <- trellis.par.get("box.rectangle")$col
trellis.par.set(list("plot.symbol" = list("col" = "black"), "box.umbrella" = list("col" = plines$col), "box.rectangle" = list("col" = ppolygons$border)))
on.exit(trellis.par.set(list("plot.symbol" = list("col" = oldcolsymbol), "box.umbrella" = list("col" = oldcolumbrella), "box.rectangle" = list("col" = oldcolrectangle))))
## manage string rotation
srt <- 0
if(is.numeric(plabels$srt[1]))
srt <- plabels$srt[1]
else {
if(plabels$srt[1] == "horizontal")
srt <- 0
else if(plabels$srt[1] == "vertical")
srt <- 90
}
gettextpos <- function(x, lim) {
if(length(x) != 2) {
## if no data in the given level
return(c(NA, NA))
} else {
if(abs(lim[2] - x[2]) > abs(lim[1] - x[1]))
return(c(x[2], 1))
else
return(c(x[1], -1))
}
}
if(pscore$horizontal) {
## horizontal plot
ylab <- at
if(length(ylab) > 1)
bwid <- diff(range(ylab)) / (nlev + 1)
else
bwid <- 1 / 10
## panel.bwplot
do.call("panel.bwplot", list(x = y, y = ylab[fac], box.ratio = bwid, coef = 1.5, pch = "|", horizontal = TRUE))
## add means
do.call("panel.points", c(list(x = (tapply(y, fac, mean)), y = ylab), ppoints))
minmax <- tapply(y, fac, range)
etis <- sapply(minmax, gettextpos, lim = lims$xlim)
} else {
## vertical plot
xlab <- at
if(length(xlab) > 1)
bwid <- diff(range(xlab)) / (nlev + 1)
else
bwid <- 1 / 10
## panel.bwplot
do.call("panel.bwplot", list(x = xlab[fac], y = y, box.ratio = bwid, coef = 1.5, pch = "|", horizontal = FALSE))
## add means
do.call("panel.points", c(list(y = (tapply(y, fac , mean)), x = xlab), ppoints))
minmax <- tapply(y, fac, range)
etis <- sapply(minmax, gettextpos, lim = lims$ylim)
}
## draw labels
if(abs(sin(srt)) > sin(45)) {
## almost vertical labels
if(pscore$horizontal)
width <- stringWidth("h")
else
width <- stringWidth(labels) + stringWidth("h")
width <- rep(plabels$cex, length.out = length(labels)) * convertUnit(width, "native", typeFrom = "dimension", axisFrom = "x", axisTo = "y", valueOnly = TRUE) / 2
} else {
## almost horizontal labels
if(pscore$horizontal)
width <- stringWidth(labels) + stringWidth("h")
else
width <- stringWidth("h")
width <- rep(plabels$cex, length.out = length(labels)) * convertUnit(width, "native", typeFrom = "dimension", axisFrom = "x", valueOnly = TRUE) / 2
}
if(pscore$horizontal)
adeg.panel.label(x = etis[1, ] + etis[2, ] * width, y = ylab, labels = labels, plabels = plabels)
else
adeg.panel.label(x = xlab, y = etis[1, ] + etis[2, ] * width, labels = labels, plabels = plabels)
})
## For boxplot, parameters can only be changed using par.settings arguments;
setMethod(
f = "setlatticecall",
signature = "S1.boxplot",
definition = function(object) {
name_obj <- deparse(substitute(object))
callNextMethod()
ppolygons <- object@adeg.par$ppolygons
object@lattice.call$arguments$par.settings <- modifyList(list(box.rectangle = c(list(col = ppolygons$border, fill = ppolygons$col),
ppolygons[-c(which(names(ppolygons) == "border" | (names(ppolygons) == "col")))]), box.umbrella = object@adeg.par$plines,
plot.symbol = modifyList(list(col = "black", fill = "black"), object@adeg.par$ppoints)), object@lattice.call$arguments$par.settings, keep.null = TRUE)
assign(name_obj, object, envir = parent.frame())
})
s1d.boxplot <- function(score, fac = gl(1, NROW(score)), at = 1:nlevels(fac), col = NULL, facets = NULL, plot = TRUE, storeData = TRUE, add = FALSE, pos = -1, ...) {
## evaluation of some parameters
thecall <- .expand.call(match.call())
fac <- eval(thecall$fac, envir = sys.frame(sys.nframe() + pos))
score <- eval(thecall$score, envir = sys.frame(sys.nframe() + pos))
if(NROW(fac) != NROW(score))
stop("fac and score must have the same number of rows")
## parameters sorted
sortparameters <- sortparamADEg(...)
## facets
if(!is.null(facets)) {
if(NCOL(score) == 1 & NCOL(fac) == 1)
object <- multi.facets.S1(thecall, sortparameters$adepar, samelimits = sortparameters$g.args$samelimits)
else
stop("Facets are not allowed with multiple scores or fac")
}
## multiple scores
else if(NCOL(score) > 1) {
if(NCOL(fac) == 1)
object <- multi.score.S1(thecall)
else
stop("Multiple scores are not allowed with multiple fac")
}
## multiple fac
else if(NCOL(fac) > 1) {
object <- multi.variables.S1(thecall, "fac")
}
## 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$g.args, list(col = col))
if(storeData)
tmp_data <- list(score = score, fac = fac, at = at, frame = sys.nframe() + pos, storeData = storeData)
else
tmp_data <- list(score = thecall$score, fac = fac, at = thecall$at, frame = sys.nframe() + pos, storeData = storeData)
object <- new(Class = "S1.boxplot", data = tmp_data, adeg.par = sortparameters$adepar, trellis.par = sortparameters$trellis, g.args = g.args, Call = match.call())
## preparation
prepare(object)
setlatticecall(object)
if(add)
object <- add.ADEg(object)
}
if(!add & plot)
print(object)
invisible(object)
}
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