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lines2D <- function(x, y, ...) {
dot <- list(...)
if (is.null(dot$type))
dot$type <- "l"
do.call("scatter2D", c(alist(x, y), dot))
}
points2D <- function(x, y, ...) {
dot <- list(...)
if (is.null(dot$type))
dot$type <- "p"
do.call("scatter2D", c(alist(x, y), dot))
}
## =============================================================================
## Scatterplots (2-D)
## =============================================================================
scatter2D <- function(x, y, ..., colvar = NULL,
col = NULL, NAcol = "white", breaks = NULL,
colkey = NULL,
clim = NULL, clab = NULL, CI = NULL,
add = FALSE, plot = TRUE) {
plist <- initplist(add)
plist <- add2Dplist(plist, "scatter", x = x, y = y, colvar = colvar,
col = col, NAcol = NAcol, breaks = breaks,
colkey = colkey,
clim = clim, clab = clab, CI = CI, ...)
setplist(plist)
if (!plot) return()
dots <- splitpardots(list(...))
isCI <- is.list(CI)
if (isCI)
CI <- check.CI(CI, length(x), 2)
if (is.null(col) & is.null(breaks))
col <- jet.col(100)
else if (is.null(col))
col <- jet.col(length(breaks)-1)
breaks <- check.breaks(breaks, col)
if (! is.null(colvar)) {
if (dots$clog) {
colvar <- log(colvar)
if (! is.null(clim)) clim <- log(clim)
}
iscolkey <- is.colkey(colkey, col)
if (iscolkey) {
colkey <- check.colkey(colkey)
if (! add)
plist$plt$main <- colkey$parplt
setplist(plist)
colkey$breaks <- breaks
}
if (length(colvar) != length(x))
stop ("length of 'colvar' should be equal to length of 'x' and 'y'")
if (is.null(clim))
clim <- range(colvar, na.rm = TRUE)
if (! is.null(dots$alpha))
col <- setalpha(col, dots$alpha)
Col <- variablecol(colvar, col, NAcol, clim, breaks)
} else { # no colvar
Col <- col
if (is.null(Col))
Col <- "black"
if (! is.null(dots$alpha))
Col <- setalpha(Col, dots$alpha)
iscolkey <- FALSE
}
useSegments <- FALSE
par (plt = plist$plt$main)
if (! is.null(dots$points$type))
if (dots$points$type %in% c("b", "l", "o"))
if (length(Col) > 1 )
useSegments <- TRUE
if (useSegments) {
Type <- dots$points$type
len <- length(x)
if (Type %in% c("b", "o")) # no distinction is made..
dots$points$type <- "p"
else
dots$points$type <- "n"
# mean of point colors for line colors
LCol <- cbind(Col[-1], Col[-len])
LCol <- apply(LCol, MARGIN = 1, FUN = MeanColors)
if (! is.null(dots$alpha))
LCol <- setalpha(LCol, dots$alpha)
if (! add)
dots$main <- start2Dplot(dots$main, x, y)
add <- TRUE
if (isCI) {
plot_CI_2d(CI, x, y, Col)
isCI <- FALSE
}
do.call("points", c(alist(x, y, col = Col), dots$points))
dots$points$type <- NULL
do.call("segments", c(alist(x[-len], y[-len], x[-1], y[-1],
col = LCol), dots$points))
}
else if (! add) {
dots$main <- start2Dplot(dots$main, x, y)
if (isCI) {
plot_CI_2d(CI, x, y, Col)
isCI <- FALSE
}
do.call("points", c(alist(x, y, col = Col), dots$points))
} else {
if (isCI) {
plot_CI_2d(CI, x, y, Col)
isCI <- FALSE
}
do.call("points", c(alist(x, y, col = Col), dots$points))
}
if (iscolkey) {
drawcolkey(colkey, col, clim, clab, dots$clog)
par(plt = plist$plt$ori)
}
par(mar = par("mar"))
}
## =============================================================================
## Confidence interval check for scatters (2D and 3D)
## =============================================================================
check.CI <- function(CI, len, dim) {
if (dim == 2 & !is.null(CI$z))
stop("'CI' should not contain confidence intervals in the 'z' direction for 2-D plot")
if (dim == 2 & is.null(CI$x) & is.null(CI$y))
stop("'CI' should contain confidence intervals the 'x' and/or 'y' direction")
if (dim == 3 & (is.null(CI$x) & is.null(CI$y) & is.null(CI$z)))
stop("'CI' should contain confidence intervals in 'x', 'y', or 'z' direction")
if (!is.null(CI$x)) {
if (! is.matrix(CI$x))
stop("'CI$x' should be a matrix")
if (ncol(CI$x) != 2)
stop("'CI$x' should be a matrix with two columns, with lower and upper value")
if (nrow(CI$x) != len)
stop("number of rows of matrix 'CI$x' should be equal to number of points")
}
if (!is.null(CI$y)) {
if (! is.matrix(CI$y))
stop("'CI$y' should be a matrix")
if (ncol(CI$y) != 2)
stop("'CI$y' should be a matrix with two columns, with lower and upper value")
if (nrow(CI$y) != len)
stop("number of rows of matrix 'CI$y' should be equal to number of points")
}
if (!is.null(CI$z)) {
if (! is.matrix(CI$z))
stop("'CI$z' should be a matrix")
if (ncol(CI$z) != 2)
stop("'CI$z' should be a matrix with two columns, with lower and upper value")
if (nrow(CI$z) != len)
stop("number of rows of matrix 'CI$z' should be equal to number of points")
}
parameter <- list(alen = 0.01, lty = par("lty"), lwd = par("lwd"), col = NULL)
CIpar <- CI
CIpar$x <- CIpar$y <- CIpar$z <- NULL
CIpar <- overrulepar(parameter, CIpar)
CIpar$x <- CI$x
CIpar$y <- CI$y
CIpar$z <- CI$z
CIpar
}
## =============================================================================
## CI in 2-d
## =============================================================================
plot_CI_2d <- function(CI, x, y, Col) { # very-very simple
CIpar <- CI[c("lty", "lwd", "col")]
if (is.null(CIpar$col))
CIpar$col <- Col
if (! is.null(CI$x)) { # CI in x direction
len <- par("fin")[1] * CI$alen
do.call("arrows", c(alist(x, y, x-CI$x[, 1], y, angle = 90, length = len), CIpar))
do.call("arrows", c(alist(x, y, x+CI$x[, 2], y, angle = 90, length = len), CIpar))
}
if (! is.null(CI$y)) {
len <- par("fin")[2] * CI$alen
do.call("arrows", c(alist(x, y, x, y-CI$y[, 1], angle = 90, length = len), CIpar))
do.call("arrows", c(alist(x, y, x, y+CI$y[, 2], angle = 90, length = len), CIpar))
}
}
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