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## Modifikation of function corPlot of package MKmisc
simPlot <- function (x, col, minVal = 0.5, labels = FALSE,
lab.both.axes = FALSE, labcols = "black",
title = "", cex.title = 1.2, protocol = FALSE,
cex.axis = 0.8, cex.axis.bar = 1, signifBar = 2, ...){
n <- ncol(x)
if(nrow(x) != n) stop("nrow(x) != nrcol(x)!")
if(missing(col))
col <- colorRampPalette(brewer.pal(8, "RdYlGn"))(128)
layout(matrix(c(1, 2), 1, 2), widths = c(10, 3))
if(min(x) >= minVal){
col.nr <- trunc((round(min(x), 2) - minVal)/(1-minVal)*length(col))
minValInd <- FALSE
}else{
col.nr <- 1
x[x < minVal] <- minVal
minValInd <- TRUE
}
if(lab.both.axes)
image(1:n, 1:n, x[, n:1], col = col[col.nr:length(col)],
axes = FALSE, xlab = "", ylab = "", ...)
else
image(1:n, 1:n, x[, n:1], col = col[col.nr:length(col)],
axes = FALSE, xlab = "sample index", ylab = "", ...)
if (length(labcols) == 1) {
axis(2, at = n:1, labels = labels, las = 2, cex.axis = cex.axis,
col.axis = labcols)
axis(1, at = 1:n, labels = 1:n, las = 1, cex.axis = cex.axis,
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 = cex.axis, col.axis = cols[i])
if(lab.both.axes)
axis(1, at = which, labels = labels[which], las = 2,
cex.axis = cex.axis, col.axis = cols[i])
else
axis(1, at = which, labels = (1:n)[which], las = 2,
cex.axis = cex.axis, col.axis = cols[i])
}
}
title(title, cex.main = cex.title)
box()
x.bar <- seq(min(minVal, min(x, na.rm = TRUE)), max(x, 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[3], x.small[8]), labels = c("<-- dissimilar", "similar -->"), las = 0, cex.axis = cex.axis.bar)
}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)
if(minValInd)
Labels <- c(signif(rev(x.small[2:10]), signifBar), paste("<=", signif(x.small[1], signifBar), sep = ""))
else
Labels <- signif(rev(x.small), signifBar)
axis(4, at = rev(x.small), labels = Labels, las = 1, cex.axis = cex.axis.bar)
}
layout(1)
par(mar = c(5, 4, 4, 2) + 0.1)
invisible()
}
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