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#
# pairs.im.R
#
# $Revision: 1.22 $ $Date: 2021/06/29 03:43:35 $
#
pairs.listof <- pairs.solist <- function(..., plot=TRUE) {
argh <- expandSpecialLists(list(...), special=c("solist", "listof"))
names(argh) <- good.names(names(argh), "V", seq_along(argh))
haslines <- any(sapply(argh, inherits, what="linim"))
if(haslines) {
if(!requireNamespace("spatstat.linnet")) {
warning(paste("the pairs() plot for images on a linear network",
"requires the package 'spatstat.linnet'"),
call.=FALSE)
return(NULL)
}
do.call(spatstat.linnet::pairs.linim, append(argh, list(plot=plot)))
} else {
do.call(pairs.im, append(argh, list(plot=plot)))
}
}
pairs.im <- local({
allpixelvalues <- function(Z) { as.numeric(as.matrix(Z)) }
pairs.im <- function(..., plot=TRUE, drop=TRUE) {
argh <- list(...)
cl <- match.call()
## unpack single argument which is a list of images
if(length(argh) == 1) {
arg1 <- argh[[1]]
if(is.list(arg1) && all(unlist(lapply(arg1, is.im))))
argh <- arg1
}
## identify which arguments are images
isim <- unlist(lapply(argh, is.im))
nim <- sum(isim)
if(nim == 0)
stop("No images provided")
## separate image arguments from others
imlist <- argh[isim]
rest <- argh[!isim]
## determine image names for plotting
imnames <- argh$labels %orifnull% names(imlist)
if(length(imnames) != nim || !all(nzchar(imnames))) {
#' names not given explicitly
callednames <- paste(cl)[c(FALSE, isim, FALSE)]
backupnames <- paste0("V", seq_len(nim))
if(length(callednames) != nim) {
callednames <- backupnames
} else if(any(toolong <- (nchar(callednames) > 15))) {
callednames[toolong] <- backupnames[toolong]
}
imnames <- good.names(imnames, good.names(callednames, backupnames))
}
##
if(nim == 1) {
## one image: plot histogram
Z <- imlist[[1L]]
xname <- imnames[1L]
do.call(hist,
resolve.defaults(list(x=quote(Z), plot=plot),
rest,
list(xlab=xname,
main=paste("Histogram of", xname))))
## save pixel values
pixvals <- list(allpixelvalues(Z))
names(pixvals) <- xname
} else {
## extract pixel rasters and reconcile them
imwins <- solapply(imlist, as.owin)
names(imwins) <- NULL
rasta <- do.call(intersect.owin, imwins)
## convert images to common raster
imlist <- lapply(imlist, "[.im", i=rasta, raster=rasta, drop=FALSE)
## extract pixel values
pixvals <- lapply(imlist, allpixelvalues)
}
## combine into data frame
pixdf <- do.call(data.frame, pixvals)
## remove NA's
if(drop)
pixdf <- pixdf[complete.cases(pixdf), , drop=FALSE]
## pairs plot
if(plot && nim > 1)
do.call(pairs, resolve.defaults(list(x=quote(pixdf)),
rest,
list(labels=imnames, pch=".")))
labels <- resolve.defaults(rest, list(labels=imnames))$labels
colnames(pixdf) <- labels
class(pixdf) <- c("plotpairsim", class(pixdf))
return(invisible(pixdf))
}
pairs.im
})
plot.plotpairsim <- function(x, ...) {
xname <- short.deparse(substitute(x))
x <- as.data.frame(x)
if(ncol(x) == 1) {
x <- x[,1L]
do.call(hist.default,
resolve.defaults(list(x=quote(x)),
list(...),
list(main=xname, xlab=xname)))
} else {
do.call(pairs.default,
resolve.defaults(list(x=quote(x)),
list(...),
list(pch=".")))
}
return(invisible(NULL))
}
print.plotpairsim <- function(x, ...) {
cat("Object of class plotpairsim\n")
cat(paste("contains pixel data for", commasep(sQuote(colnames(x))), "\n"))
return(invisible(NULL))
}
panel.image <- function(x, y, ..., sigma=NULL) {
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
xx <- scaletointerval(x)
yy <- scaletointerval(y)
p <- ppp(xx, yy, window=square(1), check=FALSE)
plot(density(p, sigma=sigma), add=TRUE, ...)
}
panel.contour <- function(x, y, ..., sigma=NULL) {
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
xx <- scaletointerval(x)
yy <- scaletointerval(y)
p <- ppp(xx, yy, window=square(1), check=FALSE)
Z <- density(p, sigma=sigma)
dont.complain.about(Z)
do.call(contour,
resolve.defaults(list(x=quote(Z), add=TRUE),
list(...),
list(drawlabels=FALSE)))
}
panel.histogram <- function(x, ...) {
usr <- par("usr"); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
h <- hist(x, plot = FALSE)
breaks <- h$breaks; nB <- length(breaks)
y <- h$counts; y <- y/max(y)
do.call(rect,
resolve.defaults(list(xleft = breaks[-nB],
ybottom = 0,
xright = breaks[-1],
ytop = y),
list(...),
list(col="grey")))
}
## pairwise things like correlations
cov.im <- function(..., use = "everything",
method = c("pearson", "kendall", "spearman")) {
df <- pairs.im(..., plot=FALSE, drop=FALSE)
V <- cov(df, use=use, method=method)
return(V)
}
cor.im <- function(..., use = "everything",
method = c("pearson", "kendall", "spearman")) {
df <- pairs.im(..., plot=FALSE, drop=FALSE)
R <- cor(df, use=use, method=method)
return(R)
}
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