Description Usage Arguments Details Author(s) References Examples

Performs the stocsy analysis on the matrix deflated through the 'oplsda' function

1 |

`threshold` |
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. |

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.

Edoardo Gaude, Dimitrios Spiliotopoulos, Francesca Chignola, Silvia Mari, Andrea Spitaleri and Michela Ghitti

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | ```
## 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)
}
}
``` |

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