logical, indicating whether positive and negative threshold must be specified. By default is 'TRUE'.
pos.threshold
The positive threshold for plotting positive correlations.
neg.threshold
The negative threshold for plotting negative correlations.
Details
OSTOCSY correlation matrix is graphically visualized, with correlations ranging from -1 to 1 and color coded for negative correlations (blue), positive correlations (red) and no correlation (white). If 'threshold' is 'TRUE' an additional plot is generated with correlation values >= and =< to the specified positive and negative thresholds, respectively. All plots visualized are written in the directory 'OSTOCSY', together with the deflated (OSC-filtered) matrix.
Author(s)
Edoardo Gaude, Dimitrios Spiliotopoulos, Francesca Chignola, Silvia Mari, Andrea Spitaleri and Michela Ghitti
References
Blaise, B.J. et al. Orthogonal filtered recoupled-STOCSY to extract metabolic networkd associated with minor perturbations from NMR spectroscopy. (2011) J Proteome Res. 10(9):4342-8.
Examples
## The function is currently defined as
function (threshold = TRUE, pos.threshold, neg.threshold)
{
pwd.n = paste(getwd(), "/OPLS-DA/X_deflated.csv", sep = "")
x <- read.csv(pwd.n, sep = ",", header = TRUE)
x.x <- x[, 2:ncol(x)]
rownames(x.x) <- x[, 1]
x.t <- x.x
mycor = cor(x.t, method = c("pearson"))
library(gplots)
col = colorpanel(50, "blue", "white", "red")
image(mycor, axes = FALSE, col = col, main = "OSTOCSY")
axis(side = 1, labels = colnames(mycor), at = seq(0, 1, length = length(colnames(mycor))),
las = 2, cex.axis = 0.4)
axis(side = 2, labels = colnames(mycor), at = seq(0, 1, length = length(colnames(mycor))),
las = 2, cex.axis = 0.4)
dirout = paste(getwd(), "/OPLS-DA/OSTOCSY/", sep = "")
dir.create(dirout)
o = paste(dirout, "OSTOCSY.pdf", sep = "")
dev.copy2pdf(file = o)
o.cor = paste(dirout, "CorrelationMatrix.csv", sep = "")
write.csv(mycor, file = o.cor)
if (threshold) {
dev.new()
image(mycor, axes = FALSE, zlim = c(pos.threshold, 1),
col = "red", main = paste("OSTOCSY <", neg.threshold,
" & >", pos.threshold, sep = ""))
image(mycor, axes = FALSE, zlim = c(-1, neg.threshold),
col = "navy", add = TRUE)
axis(side = 1, labels = colnames(mycor), at = seq(0,
1, length = length(colnames(mycor))), las = 2, cex.axis = 0.4)
axis(side = 2, labels = colnames(mycor), at = seq(0,
1, length = length(colnames(mycor))), las = 2, cex.axis = 0.4)
out = paste(dirout, "OSTOCSY_", pos.threshold, "_", neg.threshold,
".pdf", sep = "")
dev.copy2pdf(file = out)
}
}