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# This function is a slightly modified version of plot.ca() from package ca.
# Released under the GPL (no version specified), Copyright Michael Greenacre
# and Oleg Nenadic <onenadi at uni-goettingen.de>.
# http://cran.r-project.org/web/packages/ca/index.html
plotCorpusCa <- function (x, dim = c(1, 2), map = "symmetric",
what = c("all", "all"), mass = c(FALSE, FALSE),
contrib = c("none", "none"), col = c("blue", "red"),
col.text = c("black", "blue", "black", "red"),
font = c(3, 4, 1, 2),
pch = c(16, 1, 17, 24), labels = c(2, 2),
arrows = c(FALSE, FALSE), cex = 0.75,
xlab = paste("Dimension", dim[1]),
ylab = paste("Dimension", dim[2]), ...)
{
obj <- x
if (length(what) != 2)
what <- rep(what, length = 2)
if (length(mass) != 2)
mass <- rep(mass, length = 2)
if (length(contrib) != 2)
contrib <- rep(contrib, length = 2)
if (length(col) != 2)
col <- rep(col, length = 2)
if (length(col.text) != 2)
col.text <- rep(col.text, length = 4)
if (length(font) != 2)
font <- rep(font, length = 4)
if (length(labels) != 2)
labels <- rep(labels, length = 2)
if (length(pch) != 4)
pch <- rep(pch, length = 4)
if (!is.numeric(x$suprow)) {
if (map == "colgab" | map == "colgreen") {
if (what[1] != "none")
what[1] <- "active"
}
}
if (!is.numeric(x$supcol)) {
if (map == "rowgab" | map == "rowgreen") {
if (what[2] != "none")
what[2] <- "active"
}
}
if (min(dim) < 0) {
swisign <- ifelse(dim < 0, -1, 1)
dim.c <- dim(obj$rowcoord)[2]
signmat <- diag(rep(swisign, length = dim.c))
obj$rowcoord <- obj$rowcoord %*% signmat
obj$colcoord <- obj$colcoord %*% signmat
dim <- abs(dim)
}
K <- dim(obj$rowcoord)[2]
I <- dim(obj$rowcoord)[1]
J <- dim(obj$colcoord)[1]
svF <- matrix(rep(obj$sv[1:K], I), I, K, byrow = TRUE)
svG <- matrix(rep(obj$sv[1:K], J), J, K, byrow = TRUE)
rpc <- obj$rowcoord * svF
cpc <- obj$colcoord * svG
symrpc <- obj$rowcoord * sqrt(svF)
symcpc <- obj$colcoord * sqrt(svG)
mt <- c("symmetric", "rowprincipal", "colprincipal", "symbiplot",
"rowgab", "colgab", "rowgreen", "colgreen")
mti <- 1:length(mt)
mtlut <- list(symmetric = list(x = rpc, y = cpc), rowprincipal = list(x = rpc,
y = obj$colcoord), colprincipal = list(x = obj$rowcoord,
y = cpc), symbiplot = list(x = symrpc, y = symcpc), rowgab = list(x = rpc,
y = obj$colcoord * obj$colmass), colgab = list(x = obj$rowcoord *
obj$rowmass, y = cpc), rowgreen = list(x = rpc, y = obj$colcoord *
sqrt(obj$colmass)), rowgreen = list(x = obj$rowcoord *
sqrt(obj$rowmass), y = cpc))
x <- mtlut[[mti[mt == map]]][[1]]
y <- mtlut[[mti[mt == map]]][[2]]
x.names <- obj$rownames
y.names <- obj$colnames
rm(mt, mti, mtlut)
indx <- dim(x)[1]
indy <- dim(y)[1]
pch.x <- rep(pch[1], dim(x)[1])
pch.y <- rep(pch[3], dim(y)[1])
coltext.x <- rep(col.text[1], dim(x)[1])
coltext.y <- rep(col.text[3], dim(y)[1])
font.x <- rep(font[1], dim(x)[1])
font.y <- rep(font[3], dim(y)[1])
pr <- c("none", "active", "passive", "all")
pri <- 1:4
if (is.na(obj$rowsup[1])) {
sup.x <- NA
act.x <- x
xn.sup <- NA
xn.act <- x.names
}
else {
sup.x <- x[obj$rowsup, , drop=FALSE]
act.x <- x[-obj$rowsup, , drop=FALSE]
pch.x[obj$rowsup] <- pch[2]
coltext.x[obj$rowsup] <- col.text[2]
font.x[obj$rowsup] <- font[2]
xn.sup <- x.names[obj$rowsup]
xn.act <- x.names[-obj$rowsup]
}
if (is.na(obj$colsup[1])) {
sup.y <- NA
act.y <- y
yn.sup <- NA
yn.act <- y.names
}
else {
sup.y <- y[obj$colsup, , drop=FALSE]
act.y <- y[-obj$colsup, , drop=FALSE]
pch.y[obj$colsup] <- pch[4]
coltext.y[obj$colsup] <- col.text[4]
font.y[obj$colsup] <- font[4]
yn.sup <- y.names[obj$colsup]
yn.act <- y.names[-obj$colsup]
}
prlut <- list(none = list(x = NA, y = NA), active = list(x = act.x,
y = act.y), supplementary = list(x = sup.x, y = sup.y),
all = list(x = x, y = y))
nameslut <- list(none = list(x.names = NA, y.names = NA),
active = list(x.names = xn.act, y.names = yn.act), supplementary = list(x.names = xn.sup,
y.names = yn.sup), all = list(x.names = x.names,
y.names = y.names))
pchlut <- list(none = list(x.pch = NA, y.pch = NA), active = list(x.pch = rep(pch[1],
dim(x)[1]), y.pch = rep(pch[3], dim(y)[1])), supplementary = list(x.pch = rep(pch[2],
dim(x)[1]), y.pch = rep(pch[4], dim(y)[1])), all = list(x.pch = pch.x,
y.pch = pch.y))
coltextlut <- list(none = list(x.coltext = NA, y.coltext = NA), active = list(x.coltext = rep(col.text[1],
dim(x)[1]), y.coltext = rep(col.text[3], dim(y)[1])), supplementary = list(x.coltext = rep(col.text[2],
dim(x)[1]), y.coltext = rep(col.text[4], dim(y)[1])), all = list(x.coltext = coltext.x,
y.coltext = coltext.y))
fontlut <- list(none = list(x.font = NA, y.font = NA), active = list(x.font = rep(font[1],
dim(x)[1]), y.font = rep(font[3], dim(y)[1])), supplementary = list(x.font = rep(font[2],
dim(x)[1]), y.font = rep(font[4], dim(y)[1])), all = list(x.font = font.x,
y.font = font.y))
x <- prlut[[pri[pr == what[1]]]][[1]]
y <- prlut[[pri[pr == what[2]]]][[2]]
x.names <- nameslut[[pri[pr == what[1]]]][[1]]
y.names <- nameslut[[pri[pr == what[2]]]][[2]]
x.pch <- pchlut[[pri[pr == what[1]]]][[1]]
y.pch <- pchlut[[pri[pr == what[2]]]][[2]]
x.coltext <- coltextlut[[pri[pr == what[1]]]][[1]]
y.coltext <- coltextlut[[pri[pr == what[2]]]][[2]]
x.font <- fontlut[[pri[pr == what[1]]]][[1]]
y.font <- fontlut[[pri[pr == what[2]]]][[2]]
if (is.matrix(x)) {
x <- x[, dim, drop=FALSE]
}
else {
x <- matrix(x[dim], ncol = length(dim), nrow = 1)
}
if (is.matrix(y)) {
y <- y[, dim, drop=FALSE]
}
else {
y <- matrix(y[dim], ncol = length(dim), nrow = 1)
}
if (mass[1])
cex.x <- 0.5 + obj$rowmass^(1/3)/max(obj$rowmass^(1/3))
else cex.x <- 1
if (mass[2])
cex.y <- 0.5 + obj$colmass^(1/3)/max(obj$colmass^(1/3))
else cex.y <- 1
# For supplementary points with mass NA
cex.x[is.na(cex.x)] <- 1
cex.y[is.na(cex.y)] <- 1
nc0 <- 50
cst <- 230
col.x <- col[1]
col.y <- col[2]
if (contrib[1] == "relative") {
cind <- obj$rowmass * (rpc[, dim[1]]^2 + rpc[, dim[2]]^2)/obj$rowinertia
cb.x <- col2rgb(col[1])
collut.x <- rgb(seq(cst, cb.x[1, 1], length = nc0), seq(cst,
cb.x[2, 1], length = nc0), seq(cst, cb.x[3, 1], length = nc0),
maxColorValue = 255)
xtemp <- nc0 * (cind)
col.x <- collut.x[xtemp]
}
else if (contrib[1] == "absolute") {
cind <- obj$rowmass * (rpc[, dim[1]]^2 + rpc[, dim[2]]^2)/(obj$sv[dim[1]]^2 +
obj$sv[dim[2]]^2)
cb.x <- col2rgb(col[1])
p.x <- cb.x[, 1] + (cst - cb.x[, 1])/indx
collut.x1 <- rgb(seq(cst, p.x[1], length = nc0/2), seq(cst,
p.x[2], length = nc0/2), seq(cst, p.x[3], length = nc0/2),
maxColorValue = 255)
collut.x2 <- rgb(seq(p.x[1], cb.x[1, 1], length = nc0/2),
seq(p.x[2], cb.x[2, 1], length = nc0/2), seq(p.x[3],
cb.x[3, 1], length = nc0/2), maxColorValue = 255)
collut.x <- c(collut.x1, collut.x2)
xtemp <- nc0 * (cind)
col.x <- collut.x[xtemp]
}
if (contrib[2] == "relative") {
cind <- obj$colmass * (cpc[, dim[1]]^2 + cpc[, dim[2]]^2)/obj$colinertia
cb.y <- col2rgb(col[2])
collut.y <- rgb(seq(cst, cb.y[1, 1], length = nc0), seq(cst,
cb.y[2, 1], length = nc0), seq(cst, cb.y[3, 1], length = nc0),
maxColorValue = 255)
ytemp <- nc0 * cind
col.y <- collut.y[ytemp]
}
if (contrib[2] == "absolute") {
cind <- obj$colmass * (cpc[, dim[1]]^2 + cpc[, dim[2]]^2)/(obj$sv[dim[1]]^2 +
obj$sv[dim[2]]^2)
cb.y <- col2rgb(col[2])
p.y <- cb.y[, 1] + (cst - cb.y[, 1])/indy
collut.y1 <- rgb(seq(cst, p.y[1], length = nc0/2), seq(cst,
p.y[2], length = nc0/2), seq(cst, p.y[3], length = nc0/2),
maxColorValue = 255)
collut.y2 <- rgb(seq(p.y[1], cb.y[1, 1], length = nc0/2),
seq(p.y[2], cb.y[2, 1], length = nc0/2), seq(p.y[3],
cb.y[3, 1], length = nc0/2), maxColorValue = 255)
collut.y <- c(collut.y1, collut.y2)
ytemp <- nc0 * cind
col.y <- collut.y[ytemp]
}
q1 <- (1:dim(x)[1])
q2 <- (1:dim(y)[1])
l1 <- c(x[q1, 1], y[q2, 1])
l1 <- l1[!is.na(l1)]
l2 <- c(x[q1, 2], y[q2, 2])
l2 <- l2[!is.na(l2)]
if (length(l1) == 0)
l1 <- c(-0.1, 0.1)
if (length(l2) == 0)
l2 <- c(-0.1, 0.1)
lim1 <- range(l1) + c(-0.05, 0.05) * diff(range(l1))
lim2 <- range(l2) + c(-0.05, 0.05) * diff(range(l2))
pty.backup <- par()$pty
plot(c(x[, 1], y[, 1]), c(x[, 2], y[, 2]), xlab = xlab, ylab = ylab,
type = "n", axes = FALSE, asp = 1, ...)
box()
abline(h = 0, v = 0, lty = 3)
axis(1)
axis(2)
if (!is.na(x[1]) & labels[1] != 1) {
if (arrows[1]) {
arrows(rep(0, length(x[, 1])), rep(0, length(x[,
1])), x[, 1], x[, 2], col = col.x, length = 0.1)
}
else {
points(x[, 1], x[, 2], cex = cex.x, col = col.x,
pch = x.pch)
}
}
if (!is.na(y[1]) & labels[2] != 1) {
if (arrows[2]) {
arrows(rep(0, length(y[, 1])), rep(0, length(y[,
1])), y[, 1], y[, 2], col = col.y, length = 0.1)
}
else {
points(y[, 1], y[, 2], cex = cex.y, col = col.y,
pch = y.pch)
}
}
if (labels[1] > 0 && !is.na(x[1]) &&
labels[2] > 0 && !is.na(y[1]))
.pointLabel(rbind(x, y), c(x.names, y.names), cex = cex * par("cex"), xpd = TRUE,
col=c(x.coltext, y.coltext), font=c(x.font, y.font))
else if (labels[1] > 0 && !is.na(x[1]))
.pointLabel(x, x.names, cex = cex * par("cex"), xpd = TRUE, col=x.coltext, font=x.font)
else if (labels[2] > 0 && !is.na(y[1]))
.pointLabel(y, y.names, cex = cex * par("cex"), xpd = TRUE, col=y.coltext, font=y.font)
par(pty = pty.backup)
}
# Function taken from the directlabels package, but it is in the public domain
.pointLabel <- function(x, y = NULL, labels = seq(along = x), cex = 1,
method = c("SANN", "GA"),
allowSmallOverlap = FALSE,
trace = FALSE,
doPlot = TRUE,
...)
{
# http://en.wikipedia.org/wiki/Automatic_label_placement
# http://www.szoraster.com/Cartography/PracticalExperience.htm
# http://www.eecs.harvard.edu/~shieber/Projects/Carto/carto.html
# http://i11www.iti.uni-karlsruhe.de/map-labeling/bibliography/
if (!missing(y) && (is.character(y) || is.expression(y))) {
labels <- y
y <- NULL
}
if (is.factor(labels))
labels <- as.character(labels)
z = xy.coords(x, y, recycle = TRUE)
x = z$x
y = z$y
if (length(labels) < length(x))
labels = rep(labels, length(x))
method <- match.arg(method)
boundary = par()$usr
image_width = boundary[2] - boundary[1]
image_height = boundary[4] - boundary[3]
if (allowSmallOverlap) # default to 2% of the image size
nudgeFactor = .02*(abs(boundary[1] + 1i*boundary[2] - boundary[3] - 1i*boundary[4]))
n_labels = length(x)
# There are eight possible alignment codes, corresponding to the
# corners and side mid-points of the rectangle
# Codes are 1:8
# Code 7 is the most preferred
xBoundary = image_width * 0.01 # add a small boundary around the rectangle
yBoundary = image_height * 0.01
width = strwidth(labels, units = "user", cex = cex) + xBoundary
height = strheight(labels, units = "user", cex = cex) + yBoundary
gen_offset <- function(code)
c(-1, -1, -1, 0, 0, 1, 1, 1)[code] * (width/2) +
1i * c(-1, 0, 1, -1, 1, -1, 0, 1)[code] * (height/2)
# Finds intersection area of two rectangles
rect_intersect <- function(xy1, offset1, xy2, offset2) {
w = pmin(Re(xy1+offset1/2), Re(xy2+offset2/2)) - pmax(Re(xy1-offset1/2), Re(xy2-offset2/2))
h = pmin(Im(xy1+offset1/2), Im(xy2+offset2/2)) - pmax(Im(xy1-offset1/2), Im(xy2-offset2/2))
w[w <= 0] = 0
h[h <= 0] = 0
w*h
}
nudge <- function(offset) {
# Nudge the labels slightly if they overlap:
doesIntersect = rect_intersect(xy[rectidx1] + offset[rectidx1], rectv[rectidx1],
xy[rectidx2] + offset[rectidx2], rectv[rectidx2]) > 0
pyth = abs(xy[rectidx1] + offset[rectidx1] - xy[rectidx2] - offset[rectidx2]) / nudgeFactor
eps = 1.0e-10
for (i in which(doesIntersect & pyth > eps)) {
idx1 = rectidx1[i]
idx2 = rectidx2[i]
vect = (xy[idx1] + offset[idx1] - xy[idx2] - offset[idx2]) / pyth[idx1]
offset[idx1] = offset[idx1] + vect
offset[idx2] = offset[idx2] - vect
}
offset
}
objective <- function(gene) {
offset = gen_offset(gene)
# Allow for "bending" the labels a bit
if (allowSmallOverlap) offset = nudge(offset)
if (!is.null(rectidx1))
area = sum(rect_intersect(xy[rectidx1] + offset[rectidx1], rectv[rectidx1],
xy[rectidx2] + offset[rectidx2], rectv[rectidx2]))
else
area = 0
# Penalize labels which go outside the image area
# Count points outside of the image
n_outside = sum(Re(xy + offset - rectv/2) < boundary[1] | Re(xy + offset + rectv/2) > boundary[2] |
Im(xy + offset - rectv/2) < boundary[3] | Im(xy + offset + rectv/2) > boundary[4])
area + n_outside * image_width * image_height
}
# Make a list of label rectangles in their reference positions,
# centered over the map feature; the real labels are displaced
# from these positions so as not to overlap
# Note that some labels can be bigger than others
xy = x + 1i * y
rectv = width + 1i * height
rectidx1 = rectidx2 = array(0, (length(x)^2 - length(x)) / 2)
k=0
for (i in 1:length(x))
for (j in seq(len=(i-1))) {
k = k + 1
rectidx1[k] = i
rectidx2[k] = j
}
canIntersect = rect_intersect(xy[rectidx1], 2 * rectv[rectidx1],
xy[rectidx2], 2 * rectv[rectidx2]) > 0
rectidx1 = rectidx1[canIntersect]
rectidx2 = rectidx2[canIntersect]
if (trace) cat("possible intersects =", length(rectidx1), "\n")
if (trace) cat("portion covered =", sum(rect_intersect(xy, rectv,xy,rectv))/(image_width*image_height),"\n")
SANN <- function() {
# Make some starting "genes"
#gene = sample(1:8, n_labels, repl = TRUE)
gene = rep(8, n_labels)
score = objective(gene)
bestgene = gene
bestscore = score
T = 2.5
for (i in 1:50) {
k = 1
for (j in 1:50) {
newgene = gene
newgene[sample(1:n_labels, 1)] = sample(1:8,1)
newscore = objective(newgene)
if (newscore < score || runif(1) < 1 - exp((newscore - score) / T)) {
k = k + 1
score = newscore
gene = newgene
}
if (score <= bestscore) {
bestscore = score
bestgene = gene
}
if (bestscore == 0 || k == 10) break
}
if (bestscore == 0) break
if (trace) cat("overlap area =", bestscore, "\n")
T = 0.9 * T
}
if (trace) cat("overlap area =", bestscore, "\n")
nx = Re(xy + gen_offset(bestgene))
ny = Im(xy + gen_offset(bestgene))
list(x = nx, y = ny)
}
xy = SANN()
if (doPlot)
text(xy, labels, cex = cex, ...)
invisible(xy)
}
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