Nothing
####################################################
## Uni-dimensionnal plot ##
####################################################
setClass(
Class = "ADEg.S1",
contains = c("ADEg", "VIRTUAL"),
slots = c(data = "list")
)
setMethod(
f = "initialize",
signature = "ADEg.S1",
definition = function(.Object, data = list(score = NULL, at = NULL, frame = 0, storeData = TRUE), ...) {
.Object <- callNextMethod(.Object, ...) ## ADEg initialize
.Object@data <- data
return(.Object)
})
## prepare: grid calculations
## reset limits and sets axis information for lattice
setMethod(
f = "prepare",
signature = "ADEg.S1",
definition = function(object) {
name_obj <- deparse(substitute(object))
if(object@data$storeData) {
score <- object@data$score
at <- object@data$at
} else {
score <- eval(object@data$score, envir = sys.frame(object@data$frame))
at <- eval(object@data$at, envir = sys.frame(object@data$frame))
}
if(inherits(object, "S1.boxplot")){
if(object@data$storeData) {
fac <- object@data$fac
} else {
fac <- eval(object@data$fac, envir = sys.frame(object@data$frame))
}
}
score <- as.matrix(score)[, 1] ## to manage 'score' when it is a data.frame with only one column
## limits and scale
minX <- min(score)
maxX <- max(score)
if(object@adeg.par$p1d$horizontal & !is.null(object@g.args$xlim) & is.null(object@s.misc$hori.update)) {
minX <- object@g.args$xlim[1]
maxX <- object@g.args$xlim[2]
}
if(!object@adeg.par$p1d$horizontal & !is.null(object@g.args$ylim) & is.null(object@s.misc$hori.update)) {
minX <- object@g.args$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) || !identical(object@s.misc$hori.update, object@adeg.par$p1d$horizontal))
object@g.args$xlim <- lim
if(is.null(object@g.args$ylim))
object@g.args$ylim <- setlimits1D(min(at), max(at), 0, FALSE)
if(inherits(object, "S1.boxplot")) ## extend ylim for boxes
object@g.args$ylim <- object@g.args$ylim + c(-1, 1) * abs(diff(range(at))) / (nlevels(fac) + 1)
ref <- ifelse(object@adeg.par$p1d$reverse, 2, 1)
margin <- object@g.args$ylim[ref]
if(object@adeg.par$p1d$rug$draw)
margin <- object@adeg.par$p1d$rug$margin * abs(diff(object@g.args$ylim))
object@s.misc$rug <- object@g.args$ylim[ref]
object@g.args$ylim[ref] <- object@g.args$ylim[ref] + lead * margin
} 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$ylim) || !identical(object@s.misc$hori.update, object@adeg.par$p1d$horizontal))
object@g.args$ylim <- lim
if(is.null(object@g.args$xlim))
object@g.args$xlim <- setlimits1D(min(at), max(at), 0, FALSE)
if(inherits(object, "S1.boxplot")) ## extend xlim for boxes
object@g.args$xlim <- object@g.args$xlim + c(-1, 1) * abs(diff(range(at))) / (nlevels(fac) + 1)
ref <- ifelse(object@adeg.par$p1d$reverse, 2, 1)
margin <- object@g.args$xlim[ref]
if(object@adeg.par$p1d$rug$draw)
margin <- object@adeg.par$p1d$rug$margin * abs(diff(object@g.args$xlim))
object@s.misc$rug <- object@g.args$xlim[ref]
object@g.args$xlim[ref] <- object@g.args$xlim[ref] + lead * margin
}
object@g.args$scales <- scalesandlab
object@s.misc$hori.update <- object@adeg.par$p1d$horizontal
assign(name_obj, object, envir = parent.frame())
})
setMethod(
f = "panelbase",
signature = "ADEg.S1",
definition = function(object, x, y) {
## Formula defined in gettrellis
## if horizontal, x is score and y is a vector with repetitions of origin
## if vertical, this is the inverse
grid <- object@adeg.par$pgrid
porigin <- object@adeg.par$porigin
pscore <- object@adeg.par$p1d
lims <- current.panel.limits(unit = "native")
plines <- object@adeg.par$plines
if(!is.null(object@data$fac)) {
## there is a factor in the data (e.g., S1.class)
if(object@data$storeData)
fac <- object@data$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$reverse, object@g.args$ylim[2], object@g.args$ylim[1])
margin <- ref
if(pscore$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$line) object@s.misc$rug 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 <- object@s.misc$rug
end <- start - pscore$rug$tck * lead * abs(start - ref)
## 'panel.rug' needs 'npc' values
start <- convertUnit(unit(start, "native"), unitTo = "npc", axisFrom = "y", valueOnly = TRUE)
end <- convertUnit(unit(end, "native"), unitTo = "npc", axisFrom = "y", valueOnly = TRUE)
do.call("panel.rug", c(list(x = y, start = start, end = end), plines))
}
} else {
## vertical plot
## set margins to get some place for rug
ref <- ifelse(pscore$reverse, object@g.args$xlim[2], object@g.args$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) object@s.misc$rug else NULL,
col = porigin$col, lwd = porigin$lwd, lty = porigin$lty, alpha = porigin$alpha)
## draw rug
if(pscore$rug$draw && (pscore$rug$tck != 0)) {
## tick end and starting points
start <- object@s.misc$rug
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$col, alpha = 0.8, col = "transparent"))
grid.draw(textgrid)
}
callNextMethod()
})
setMethod(
f = "setlatticecall",
signature = "ADEg.S1",
definition = function(object) {
## arguments recurrents de la liste, pas les limites car elles seront definis ensuite
name_obj <- deparse(substitute(object))
## grid background and box
object@trellis.par$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 S1.panel function, for slabel and ADEg.S1 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.S1",
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))
fml <- as.formula(score ~ xdata)
tmptrellis <- do.call(what = object@lattice.call$graphictype, args = c(fml, object@lattice.call$arguments, environment()))
return(tmptrellis)
})
## zoom without center
setMethod(
f = "zoom",
signature = c("ADEg.S1", "numeric", "missing"),
definition = function(object, zoom, center) {
## zoom in xlim
p1d <- object@adeg.par$p1d
nameobj <- deparse(substitute(object))
if(length(zoom) != 1)
stop("zoom factor should be length 1")
center <- ifelse(p1d$horizontal, mean(object@g.args$xlim), mean(object@g.args$ylim))
zoom(object, zoom, center)
})
## zoom with center
setMethod(
f = "zoom",
signature = c("ADEg.S1", "numeric", "numeric"),
definition = function(object, zoom, center) {
nameobj <- deparse(substitute(object))
p1d <- object@adeg.par$p1d
origin <- object@adeg.par$porigin
if(length(center) != 1)
stop("Center should be a numeric")
if(length(zoom) != 1)
stop("Zoom factor should be a numeric")
if(p1d$horizontal) {
diffx <- diff(object@g.args$xlim) / zoom
minX <- center - diffx / 2
maxX <- center + diffx / 2
object@g.args$xlim <- c(minX, maxX)
} else {
diffx <- diff(object@g.args$ylim) / zoom
minX <- center - diffx / 2
maxX <- center + diffx / 2
object@g.args$ylim <- c(minX, maxX)
}
lim <- setlimits1D(minX, maxX, origin = origin$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]])
object@s.misc$backgrid <- list(x = v0, d = cgrid)
setlatticecall(object)
print(object)
invisible()
})
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