Nothing
"plot.dmat" <-
function(x,
key = TRUE,
resnum.1 = c(1:ncol(x)),
resnum.2 = resnum.1,
axis.tick.space = 20,
zlim = range(x, finite = TRUE),
nlevels = 20,
levels = pretty(zlim, nlevels),
color.palette = bwr.colors,
col = color.palette(length(levels) -1),
axes = TRUE,
key.axes,
xaxs = "i",
yaxs = "i",
las = 1,
grid = TRUE,
grid.col = "yellow",
grid.nx = floor(ncol(x)/30),
grid.ny = grid.nx,
center.zero = TRUE,
flip=TRUE,
...) {
if (missing(x)) {
stop("no 'x' distance matrix specified")
}
if(center.zero) {
if(zlim[1]<0) {
## make levels equidistant around 0
levels = pretty(c(-max(abs(zlim)),max(abs(zlim))), nlevels)
}
}
mar.orig <- (par.orig <- par(c("mar", "las", "mfrow")))$mar
on.exit(par(par.orig))
# Color key
if(key) {
w <- (3 + mar.orig[2]) * par("csi") * 2.54
layout(matrix(c(2, 1), ncol = 2), widths = c(1, lcm(w)))
par(las = las)
mar <- mar.orig
mar[4] <- mar[2]
mar[2] <- 1
par(mar = mar)
plot.new()
plot.window(xlim = c(0, 1), ylim = range(levels),
xaxs = "i", yaxs = "i")
rect(0, levels[-length(levels)], 1, levels[-1], col = col)
if (missing(key.axes)) {
if (axes)
axis(4)
}
else key.axes
box()
}
# Matrix plot
mar <- mar.orig
mar[4] <- 1
par(mar = mar)
class(x)=NULL
z <- as.matrix(as.data.frame(t(x)))
nums <- seq(1,ncol(x),by=axis.tick.space)
if(flip) {
ylim = c(ncol(z),1)
} else {
ylim = c(1,ncol(z))
}
image(x=1:ncol(x),
y=1:nrow(x),
z=z,
zlim=zlim,
col=col, yaxt="n", xaxt="n", ...)
#xlab="Residue Number", ylab="Residue Number")
axis(side=1, at=nums, labels=resnum.1[nums])
axis(side=2, at=nums, labels=resnum.2[nums])
if(grid)
grid(grid.nx ,grid.ny, col=grid.col)
box()
}
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