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## Modifikation of function plot.cor of package "sma"
madPlot <- function (x, new = FALSE, col, maxMAD = 3, labels = FALSE,
labcols = "black", title = "", protocol = FALSE, ...){
n <- ncol(x)
MAD <- x
if(new) MAD <- madMatrix(x)
if(missing(col))
col <- rev(colorRampPalette(brewer.pal(8, "RdYlGn"))(128))
if(protocol)
layout(matrix(c(1, 2), 1, 2), widths = c(10, 3))
else
layout(matrix(c(1, 2), 1, 2), widths = c(10, 2.5))
if(max(MAD) < maxMAD)
col.nr <- trunc(round(max(MAD), 2)/maxMAD*length(col))
else
col.nr <- 1
image(1:n, 1:n, MAD[, n:1], col = col[1:col.nr], axes = FALSE,
xlab = "sample index", ylab = "", ...)
if (length(labcols) == 1) {
axis(2, at = n:1, labels = labels, las = 2, cex.axis = 0.8,
col.axis = labcols)
axis(1, at = 1:n, labels = 1:n, las = 1, cex.axis = 0.8,
col.axis = labcols)
}
if (length(labcols) == n) {
cols <- unique(labcols)
for (i in 1:length(cols)) {
which <- (1:n)[labcols == cols[i]]
axis(2, at = (n:1)[which], labels = labels[which],
las = 2, cex.axis = 0.8, col.axis = cols[i])
axis(1, at = which, labels = labels[which], las = 2,
cex.axis = 0.8, col.axis = cols[i])
}
}
title(title)
box()
x.bar <- seq(0, max(maxMAD, max(MAD, na.rm = TRUE)), length = length(col))
x.small <- seq(x.bar[1], x.bar[length(x.bar)], length = 10)
par(mar = c(5.1, 1, 4.1, 5))
if(protocol){
image(1, x.bar, matrix(x.bar, 1, length(x.bar)), axes = FALSE, xlab = "", ylab = "", col = col, ...)
box()
axis(4, at = c(x.small[2], x.small[9]), labels = c("dissimilar", "similar "), las = 2)
}else{
image(1, x.bar, matrix(x.bar, 1, length(x.bar)), axes = FALSE, xlab = "", ylab = "", col = col, ...)
box()
x.small <- seq(x.bar[1], x.bar[length(x.bar)], length = 10)
Labels <- signif(rev(x.small), 2)
axis(4, at = rev(x.small), labels = Labels, las = 1)
}
layout(1)
par(mar = c(5, 4, 4, 2) + 0.1)
invisible()
}
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