Nothing
####################################################
## Curves Plot ##
## 1d score represents in 2D plot ##
####################################################
setClass(
Class = "ADEg.C1",
contains = c("ADEg", "VIRTUAL"),
slots = c(data = "list")
)
setMethod(
f = "initialize",
signature = "ADEg.C1",
definition = function(.Object, data = list(score = NULL, frame = 0, storeData = TRUE), ...) {
.Object <- callNextMethod(.Object, ...) ## ADEg initialize
.Object@data <- data
return(.Object)
})
setMethod(
f = "prepare",
signature = "ADEg.C1",
definition = function(object) {
## prepare: grid calculations
## reset limits and sets axis information for lattice
name_obj <- deparse(substitute(object))
if(object@data$storeData)
score <- object@data$score
else
score <- eval(object@data$score, envir = sys.frame(object@data$frame))
if(inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval"))
if(object@data$storeData)
at <- object@data$at
else
at <- eval(object@data$at, envir = sys.frame(object@data$frame))
score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column
if(class(object) == "C1.interval") ## to manage only the first score in c(score1, score2)
score <- score[1:(length(score) / 2)]
## limits and scale
if(!is.null(object@s.misc$hori.update))
if(object@s.misc$hori.update != object@adeg.par$p1d$horizontal) {
aux <- object@g.args$xlim
object@g.args$xlim <- object@g.args$ylim
object@g.args$ylim <- aux
}
object@s.misc$hori.update <- object@adeg.par$p1d$horizontal
minX <- min(score)
maxX <- max(score)
if(object@adeg.par$p1d$horizontal & !is.null(object@g.args$xlim)) {
minX <- object@g.args$xlim[1]
maxX <- object@g.args$xlim[2]
}
if(!object@adeg.par$p1d$horizontal & !is.null(object@g.args$ylim)) {
minX <- object@g.args$ylim[1]
maxX <- object@g.args$ylim[2]
}
origin <- object@adeg.par$porigin
lim <- setlimits1D(minX, maxX, origin = origin$origin[1], includeOr = origin$include)
## compute grid size
tmp <- pretty(lim, n = object@adeg.par$pgrid$nint)
if(!origin$include)
origin$origin[1] <- tmp[1]
cgrid <- diff(tmp)[1]
if(is.na(cgrid))
stop("error while calculating grid")
## compute grid location
v0 <- origin$origin[1]
if((origin$origin[1] + cgrid) <= lim[2])
v0 <- c(v0, seq(origin$origin[1] + cgrid, lim[2], by = cgrid))
if((origin$origin[1] - cgrid >= lim[1]))
v0 <- c(v0, seq(origin$origin[1] - cgrid, lim[1], by = -cgrid))
v0 <- sort(v0[v0 >= lim[1] & v0 <= lim[2]])
## clean near-zero values
delta <- diff(range(v0))/object@adeg.par$pgrid$nint
if (any(small <- abs(v0) < 1e-14 * delta))
v0[small] <- 0
object@s.misc$backgrid <- list(x = v0, d = cgrid)
## object@adeg.par$paxes has priority over object@g.args$scales
scalesandlab <- modifyList(as.list(object@g.args$scales), object@adeg.par$paxes, keep.null = TRUE)
if(!scalesandlab$draw) {
scalesandlab$x$draw <- FALSE
scalesandlab$y$draw <- FALSE
}
lead <- ifelse(object@adeg.par$p1d$reverse, 1 , -1)
if(object@adeg.par$p1d$horizontal) {
## draw axes for horizontal plot
if(is.null(scalesandlab$x$at))
scalesandlab$x$at <- object@s.misc$backgrid$x
if(is.null(object@g.args$xlim))
object@g.args$xlim <- lim
if(inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval"))
if(!is.null(at))
scalesandlab$y$at <- at
if(is.null(scalesandlab$y$at))
scalesandlab$y$at <- 1:NROW(score)
} else {
## draw axes for vertical plot
if(is.null(scalesandlab$y$at))
scalesandlab$y$at <- object@s.misc$backgrid$x
if(is.null(object@g.args$ylim))
object@g.args$ylim <- lim
if(inherits(object, "C1.curve") | inherits(object, "C1.dotplot") | inherits(object, "C1.interval"))
if(!is.null(at))
scalesandlab$x$at <- at
if(is.null(scalesandlab$x$at))
scalesandlab$x$at <- 1:NROW(score)
}
object@g.args$scales <- scalesandlab
assign(name_obj, object, envir = parent.frame())
})
setMethod(
f = "panelbase",
signature = "ADEg.C1",
definition = function(object, x, y) {
## Formula defined in gettrellis
## if horizontal, x is score and y is a vector with repetitions of origin
## if vertical, this is the inverse
grid <- object@adeg.par$pgrid
porigin <- object@adeg.par$porigin
pscore <- object@adeg.par$p1d
lims <- current.panel.limits(unit = "native")
## for rugs
if(pscore$rug$draw & (pscore$rug$tck != 0)) {
plines <- object@adeg.par$plines
if(!is.null(object@data$fac)) {
## C1.density or C1.gauss (different colors for rugs)
if(object@data$storeData)
fac <- as.factor(object@data$fac)
else
fac <- as.factor(eval(object@data$fac, envir = sys.frame(object@data$frame)))
plines <- lapply(plines, FUN = function(x) {return(rep(x, length.out = nlevels(fac))[fac])})
}
}
lead <- ifelse(pscore$reverse, -1, 1)
if(pscore$horizontal) {
## horizontal plot
## set margins to get some place for rug
ref <- ifelse(pscore$reverse, lims$ylim[2], lims$ylim[1])
margin <- ref
if(pscore$rug$draw)
margin <- ifelse(is.unit(pscore$rug$margin), convertUnit(pscore$rug$margin, typeFrom = "dimension", unitTo = "native", axisFrom = "y", valueOnly = TRUE), pscore$rug$margin)
## draw grid
if(grid$draw)
panel.segments(x0 = object@s.misc$backgrid$x , x1 = object@s.misc$backgrid$x, y0 = lims$ylim[1], y1 = lims$ylim[2], col = grid$col, lty = grid$lty, lwd = grid$lwd)
## draw origin
panel.abline(
v = if(porigin$draw) porigin$origin else NULL,
h = if(pscore$rug$draw & pscore$rug$line) ref + lead * margin else NULL,
col = porigin$col, lwd = porigin$lwd, lty = porigin$lty, alpha = porigin$alpha)
## draw rug
if(pscore$rug$draw & (pscore$rug$tck != 0)) {
## tick end and starting points
start <- ref + lead * margin
end <- (start - pscore$rug$tck * lead * abs(start - ref))
start <- convertUnit(unit(start, "native"), unitTo = "npc", axisFrom = "y", valueOnly = TRUE)
end <- convertUnit(unit(end, "native"), unitTo = "npc", axisFrom = "y", valueOnly = TRUE)
do.call("panel.rug", c(list(x = y, start = start, end = end), plines))
}
} else {
## vertical plot
## set margins to get some place for rug
ref <- ifelse(pscore$reverse, lims$xlim[2], lims$xlim[1])
margin <- ref
if(pscore$rug$draw)
margin <- ifelse(is.unit(pscore$rug$margin), convertUnit(pscore$rug$margin, typeFrom = "dimension", unitTo = "native", axisFrom = "x", valueOnly = TRUE), pscore$rug$margin)
## draw grid
if(grid$draw)
panel.segments(y0 = object@s.misc$backgrid$x , y1 = object@s.misc$backgrid$x, x0 = lims$xlim[1], x1 = lims$xlim[2], col = grid$col, lty = grid$lty, lwd = grid$lwd)
## draw origin
panel.abline(
h = if(porigin$draw) porigin$origin else NULL,
v = if(pscore$rug$draw & pscore$rug$line) ref + lead * margin else NULL,
col = porigin$col, lwd = porigin$lwd, lty = porigin$lty, alpha = porigin$alpha)
## draw rug
if(pscore$rug$draw && pscore$rug$tck != 0) {
## tick end and starting points
start <- ref + lead * margin
end <- (start - pscore$rug$tck * lead * abs(start - ref))
start <- convertUnit(unit(start, "native"), unitTo = "npc", axisFrom = "x", valueOnly = TRUE)
end <- convertUnit(unit(end, "native"), unitTo = "npc", axisFrom = "x", valueOnly = TRUE)
do.call("panel.rug", c(list(y = y, start = start, end = end), plines))
}
}
## indicate grid size (d = **)
if(grid$draw & (grid$text$cex > 0)) {
text.pos <- .setposition(grid$text$pos)
textgrid <- textGrob(label = paste("d =", object@s.misc$backgrid$d), x = text.pos$posi[1], y = text.pos$posi[2], gp = gpar(cex = grid$text$cex, col = grid$text$col), name = "gridtext")
grid.rect(x = text.pos$posi[1], y = text.pos$posi[2], width = grobWidth(textgrid), height = grobHeight(textgrid), gp = gpar(fill = object@adeg.par$pbackground$col, alpha = 0.8, col = "transparent"))
grid.draw(textgrid)
}
callNextMethod()
})
setMethod(
f = "setlatticecall",
signature = "ADEg.C1",
definition = function(object) {
## arguments recurrents de la liste, pas les limites car elles seront definis ensuite
name_obj <- deparse(substitute(object))
## grid background and box
object@trellis.par$panel.background$col <- object@adeg.par$pbackground$col
if(!object@adeg.par$pbackground$box)
object@trellis.par$axis.line$col <- "transparent"
arguments <- list(
par.settings = object@trellis.par,
scales = object@g.args$scales,
key = createkey(object),
axis = axis.L, ## see utils.R
panel = function(...) {
panelbase(object, ...) ## grid,
panel(object, ...) ## call to C1.panel function, for slabel and ADEg.C1 class of graphs
})
object@lattice.call$arguments <- arguments
object@lattice.call$graphictype <- "xyplot"
## get lattice arguments (set unspecified to NULL)
argnames <- c("main", "sub", "xlab", "ylab")
largs <- object@g.args[argnames]
names(largs) <- argnames
## add xlim and ylim if not NULL
if("xlim" %in% names(object@g.args))
largs["xlim"] <- object@g.args["xlim"]
if("ylim" %in% names(object@g.args))
largs["ylim"] <- object@g.args["ylim"]
object@lattice.call$arguments <- c(object@lattice.call$arguments, largs, list(strip = FALSE))
assign(name_obj, object, envir = parent.frame())
})
setMethod(
f = "gettrellis",
signature = "ADEg.C1",
definition = function(object) {
if(object@data$storeData)
score <- object@data$score
else
score <- eval(object@data$score, envir = sys.frame(object@data$frame))
score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column
xdata <- rep(1, length(score))
if(inherits(object, "C1.barchart")) {
xdata <- 1:length(score)
} else if(inherits(object, "C1.dotplot") | inherits(object, "C1.curve") | inherits(object, "C1.interval")) {
if(object@data$storeData)
xdata <- object@data$at
else
xdata <- eval(object@data$at, envir = sys.frame(object@data$frame))
}
fml <- as.formula(score ~ xdata)
tmptrellis <- do.call(what = object@lattice.call$graphictype, args = c(fml, object@lattice.call$arguments, environment()))
return(tmptrellis)
})
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