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## =============================================================================
## Create a color key
## =============================================================================
createKey <- function(x, clim = NULL, col = NULL, NAcol = "black") {
if (is.null(col))
col <- jet.col(100)
if (is.null(clim))
clim <- range(x)
else
x[x > max(clim) | x < min(clim)] <- NA
cmin <- clim[1]
crange <- diff(clim)
N <- length(col) -1
Col <- col[1 + trunc((x - cmin)/crange*1.00000000001*N)]
Col[is.na(x)] <- NAcol
Col
}
## =============================================================================
## wrapper around plotting functions that includes a legend
## =============================================================================
drawlegend <- function (legend, New = TRUE, pm = NULL) {
if (!legend$plot) return()
if (New)
par(new = TRUE)
usr <- par("usr")
Plt <- par(plt = legend$parleg) # legend parameters
legendargs <- formalArgs("legend")
colkeypar <- legend[names(legend)%in%legendargs]
if (is.null(colkeypar$legend))
colkeypar$legend <- ""
if (is.null(colkeypar$x))
colkeypar$x <- "center"
if (! is.null(pm))
pmar <- par(mar = pm)
plot(0, type = "n", xlim = c(0,1), ylim = c(0,1),
axes = FALSE, frame.plot = FALSE,
yaxs = "i", xaxs = "i", xlab = "", ylab = "")
do.call("legend", colkeypar)
par(plt = Plt)
par(usr = usr)
if (New)
par(new = FALSE)
if (! is.null(pm))
par(mar = pmar)
}
## =============================================================================
## Outer margins set with oma, e.g. for pairs plots
## =============================================================================
omapairs <- function(arglist, legend, legend.side = 4, oma = NULL, X = NULL, FAC = 50){
legend$plot <- FALSE
if (is.null(X))
X <- do.call("legend", legend)$rect
if (is.null(oma))
oma <- c(4, 4, if (!is.null(arglist$main)) 6 else 4, 4)
pin <- par("pin")
dh <- X$h*FAC*pin[2]/4.535
dw <- X$w*FAC*pin[1]/5.135
if (legend.side == 1) {
oma <- oma + c(dh, 0, 0, 0)
} else if (legend.side == 2) {
oma <- oma + c(0, dw, 0, 0)
} else if (legend.side == 3) {
oma <- oma + c(0, 0, dh, 0)
} else if (legend.side == 4) {
oma <- oma + c(0, 0, 0, dw)
}
oma
}
## =============================================================================
## Size of the legend and the main plot
## =============================================================================
legendsize <- function(legend, legend.side = 4, parplt = par("plt"), cex = 1) {
legendplot <- legend$plot
legend$plot <- FALSE
X <- do.call("legend", legend)$rect
cexplt <- cex
dw <- X$w
dh <- X$h
dd <- 0.02
dd2 <- 0.01 #0.12
parleg <- parplt
if (legend.side == 1) {
parplt <- parplt + c(0, 0, dh + 0.1 * cexplt[1], 0)
parleg[4] <- parplt[3] - dd2*cexplt[2]
} else if (legend.side == 2) {
parplt <- parplt + c(dw + 0.08*cexplt[1], 0, 0, 0)
parleg[2] <- parplt[1] - dd2*cexplt[2]
} else if (legend.side == 3) {
parplt <- parplt - c(0, 0, 0, dh + 0.05*cexplt[1])
parleg[3] <- parplt[4] + dd2*cexplt[2]
} else if (legend.side == 4) {
parplt <- parplt - c(0, dw + 0.02*cexplt[1], 0, 0)
parleg[1] <- parplt[2] + dd2*cexplt[2]
}
legend$plot <- ifelse(is.null(legendplot), TRUE, legendplot)
legend$parleg <- check.plt(parleg)
legend$parplt <- check.plt(parplt)
return(legend)
}
## =============================================================================
## main functions for plotting with a legend
## =============================================================================
legendplot <- function(..., legend = list(), legend.side = 4,
legend.cex = 1, legend.pars = NULL)
legend.plt( ..., method = "plot", legend = legend, legend.side = legend.side,
legend.cex = legend.cex, legend.pars = legend.pars)
legendmatplot <- function(..., legend = list(), legend.side = 4,
legend.cex = 1, legend.pars = NULL)
legend.plt(..., method = "matplot", legend = legend, legend.side = legend.side,
legend.cex = legend.cex, legend.pars = legend.pars)
legendhist <- function(..., legend = list(), legend.side = 4,
legend.cex = 1, legend.pars = NULL)
legend.plt(..., method = "hist", legend = legend, legend.side = legend.side,
legend.cex = legend.cex, legend.pars = legend.pars)
legendpairs <- function(..., legend = list(), legend.side = 4,
legend.cex = 1, legend.pars = NULL)
legend.oma(..., method = "pairs", legend = legend, legend.side = legend.side,
legend.cex = legend.cex, legend.pars = legend.pars)
legend.plt <- function(method = "plot", ..., #add = FALSE,
legend = list(), legend.side = 4, legend.cex = 1, legend.pars = NULL) {
if (method == "pairs"){
P <- legend.oma(..., method = "pairs", legend = legend, legend.side = legend.side,
legend.cex = legend.cex, legend.pars = legend.pars)
return(invisible(P))
}
if (! is.list(legend))
legend <- list(legend = legend)
arglist <- as.list(match.call(expand.dots = TRUE))
arglist[1] <- NULL
arglist[formalArgs(legend.plt)] <- NULL
if (length(inot <- which (names(arglist) == ""))) {
formalnames <- names(formals(method))
names(arglist)[inot] <- formalnames[inot]
}
plot.new()
par(new = TRUE)
pltori <- par("plt")
# if legend is only element, and this is unnamed, then it is the legend labels
if (length(inot <- which (names(legend) == ""))) {
if (length(inot) > 1)
stop(" 'legend' cannot have more than one unnamed argument")
names(legend)[inot] <- "legend"
}
if (is.null(legend$legend))
legend$legend <- ""
if (is.null(legend$x)) {
if (legend.side == 1) legend$x <- "bottom"
else if (legend.side == 2) legend$x <- "left"
else if (legend.side == 3) legend$x <- "top"
else if (legend.side == 4) legend$x <- "right"
else legend$x <- "center"
}
# normal position of legend, as in the default method
if (legend.side == 0) {
do.call(method, arglist)
do.call("legend", legend)
return(invisible(list(plt.legend = pltori, plt.main = pltori)))
}
# plotting parameters for the legend and main plot
cexplt <- rep(legend.cex, length.out = 2)
parplt <- pltori
parleg <- pltori
# determine size of the legend
if (is.null(legend.pars)) {
legend <- legendsize(legend, legend.side = legend.side, parplt = parplt, cex = cexplt)
} else {
legend$parleg <- check.plt(legend.pars$plt.legend)
legend$parplt <- check.plt(legend.pars$plt.main)
if(is.null(legend$plot)) legend$plot <- TRUE
}
drawlegend(legend, New = FALSE)#, pm = c(2,2,2,2))
par(plt = legend$parplt, new = TRUE)
do.call(method, arglist)
par(mar = par("mar"))
invisible(list(plt.legend = legend$parleg, plt.main = legend$parplt))
}
# a legend while setting the outer margins
legend.oma <- function(method = "pairs", ..., #add = FALSE,
legend = list(), legend.side = 4, legend.cex = 1, legend.pars = NULL) {
if (! is.list(legend))
legend <- list(legend = legend)
arglist <- as.list(match.call(expand.dots = TRUE))
arglist[1] <- NULL
arglist[formalArgs(legend.oma)] <- NULL
if (length(inot <- which (names(arglist) == ""))) {
formalnames <- names(formals(method))
names(arglist)[inot] <- formalnames[inot]
}
cexplt <- rep(legend.cex, length.out = 2)
# if legend is only one element, and this is unnamed, then it is the legend labels
if (length(inot <- which (names(legend) == ""))) {
if (length(inot) > 1)
stop(" 'legend' cannot have more than one unnamed argument")
names(legend)[inot] <- "legend"
}
if (is.null(legend$legend))
legend$legend <- ""
if (is.null(legend$x)){
if (legend.side == 1) legend$x <- "bottom"
if (legend.side == 2) legend$x <- "left"
if (legend.side == 3) legend$x <- "top"
if (legend.side == 4) legend$x <- "right"
}
plot.new()
# determine size of the legend
oma <- par("oma")
if (! is.null(legend.pars$oma))
arglist$oma <- legend.pars$oma
else if (is.null(arglist$oma))
arglist$oma <- omapairs(arglist, legend, legend.side)
par (oma = arglist$oma)
# Note: for unknown reason I need to call plot.new twice...
plot.new()
do.call(method, arglist)
# par(opar)
par(new = TRUE, oma = oma, mfrow = c(1,1))
plot.new()
if (is.null(legend$plot)) legend$plot <- TRUE
drawlegend(legend, New = FALSE, pm = c(2,2,2,2))
par(oma = oma)
return(invisible(list(oma = arglist$oma)))
}
## =============================================================================
## wrapper around plotting functions that includes a legend
## =============================================================================
colorkeyplot <- function(..., colorkey = list(), colorkey.side = 4)
colorkey.plt (method = "plot", ...,
colorkey = colorkey, colorkey.side = colorkey.side)
colorkeymatplot <- function(..., colorkey = list(), colorkey.side = 4)
colorkey.plt (method = "matplot", ..., # add = FALSE,
colorkey = colorkey, colorkey.side = colorkey.side)
colorkeyhist <- function(..., colorkey = list(), colorkey.side = 4)
colorkey.plt (method = "hist", ...,
colorkey = colorkey, colorkey.side = colorkey.side)
colorkeypairs <- function(..., colorkey = list(), colorkey.side = 4)
colorkey.oma (method = "pairs", ...,
colorkey = colorkey, colorkey.side = colorkey.side)
colorkey.plt <- function(method = "plot", ..., # add = FALSE,
colorkey = list(), colorkey.side = 4) {
arglist <- as.list(match.call(expand.dots=TRUE))
arglist[formalArgs(colorkey.plt)] <- NULL
arglist[1] <- NULL
if (length(inot <- which (names(arglist) == ""))) {
formalnames <- names(formals(method))
names(arglist)[inot] <- formalnames[inot]
}
plot.new()
par(new = TRUE)
pltori <- par("plt")
ck <- colorkey
ck$clim <- ck$clab <- ck$col <- ck$breaks <- ck$clog <- NULL
colkey <- check.colkey(ck)
colkey$plot <- TRUE
colkey$side <- colorkey.side
col <- colorkey$col
breaks <- colorkey$breaks
if (is.null(col))
if (is.null(breaks))
col <- jet.col(100)
else
col <- jet.col(length(breaks) - 1)
# breaks <- check.breaks(breaks, col)
if (! is.null(breaks))
clim <- range(breaks)
else
clim <- colorkey$clim
clog <- colorkey$clog
if (is.null(clog)) clog <- FALSE
# The
drawcolkey(colkey, col = col, clim = clim, clab = colorkey$clab,
clog = clog, New = FALSE)
par(plt = colkey$parplt, new = TRUE)
do.call(method, arglist)
par(mar = par("mar"))
invisible(list(plt.legend = colkey$parleg, plt.main = colkey$parplt))
}
# a color key while adjusting the outer margin
colorkey.oma <- function(method = "pairs", ..., # add = FALSE,
colorkey = list(), colorkey.side = 4) {
arglist <- as.list(match.call(expand.dots=TRUE))
arglist[formalArgs(colorkey.oma)] <- NULL
arglist[1] <- NULL
if (length(inot <- which (names(arglist) == ""))) {
formalnames <- names(formals(method))
names(arglist)[inot] <- formalnames[inot]
}
plot.new()
oma <- par("oma")
colorkey$side <- colorkey.side
ck <- colorkey
ck$clim <- ck$clab <- ck$col <- ck$breaks <- ck$clog <- NULL
colkey <- check.colkey(ck) # settings of the color key
colkey$plot <- TRUE
colkey$side <- colorkey.side
col <- colorkey$col
breaks <- colorkey$breaks
if (is.null(col))
if (is.null(breaks))
col <- jet.col(100)
else
col <- jet.col(length(breaks) - 1)
# breaks <- check.breaks(breaks, col)
if (! is.null(breaks))
clim <- range(breaks)
else
clim <- colorkey$clim
clog <- colorkey$clog
if (is.null(clog)) clog <- FALSE
# par(new = TRUE)
CP <- colkey$parleg # pars of the colorkey in plt units
if (is.null(arglist$oma))
arglist$oma <- omapairs(arglist, colkey, colorkey.side,
X = list(h = diff(CP[3:4]), w = diff(CP[1:2])), FAC = 150)
par (oma = arglist$oma)
plot.new()
do.call(method, arglist)
par(new = TRUE, mfrow = c(1,1), oma = oma, mar = c(2,1,2,2))
plot.new()
drawcolkey(colkey, col = col, clim = clim, clab = colorkey$clab,
clog = clog, New = FALSE)
par(mar = par("mar"), oma = oma)
invisible(list(oma = arglist$oma))
}
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