pathwayPlot {sigaR} | R Documentation |
Plotting the topology of a pathway's regulatory network as reconstructed from from DNA copy number and gene expression data by the pathway1sample
-function.
pathwayPlot(pFit, directed = TRUE, tWidth = 1, cWidth = 1, geWidth=10, cnWidth=10, circleDist = 1.5, gNames = NULL, main = "", remove = FALSE)
pFit |
Object of class |
directed |
A |
tWidth |
A |
cWidth |
A |
geWidth |
A |
cnWidth |
A |
circleDist |
A |
gNames |
A |
main |
The |
remove |
A |
Wessel N. van Wieringen: w.vanwieringen@vumc.nl
Van Wieringen, W.N., Van de Wiel, M.A. (2012), "Modeling the cis- and trans-effect of DNA copy number aberrations on gene expression levels in a pathway", submitted for publication.
See also pathway1sample
.
# set number of genes (p) and samples (n) p <- 10 n <- 1000 # sample cis-effects beta <- abs(rnorm(p)) # sample trans-effects Theta <- matrix(sample(c(-1,1), p^2, replace=TRUE, prob=c(0.2, 0.8)), ncol=p) * matrix(runif(p^2), ncol=p) / 4 diag(Theta) <- 1 # sample error variances Sigma <- diag(rchisq(p, df=1)/5 + 0.5) # sample DNA copy number data X <- matrix(runif(n*p, min=-2, max=2), ncol=p) # sample gene expression data Y <- t(apply(X, 1, function(Y, beta){ Y * beta }, beta=beta)) %*% t(solve(Theta)) + rmvnorm(n, sigma=solve(Theta) %*% Sigma %*% t(solve(Theta))) # fit model pFit <- pathway1sample(Y, X, lambda1=500) # plot pathway topology pathwayPlot(pFit, tWidth=5, cWidth=5)