pathwayPlot: Plot of the pathyway topology as reconstructed from from DNA...

Description Usage Arguments Author(s) References See Also Examples

View source: R/pathwayFunctions.R

Description

Plotting the topology of a pathway's regulatory network as reconstructed from from DNA copy number and gene expression data by the pathway1sample-function.

Usage

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pathwayPlot(pFit, directed = TRUE, tWidth = 1, cWidth = 1, geWidth=10, 
	cnWidth=10, circleDist = 1.5, gNames = NULL, main = "", remove = FALSE)

Arguments

pFit

Object of class pathwayFit as returned by the function pathway1sample.

directed

A logical indicating whether to plot directed or undirected trans-effects.

tWidth

A numeric that scales the width of the trans-effect edges.

cWidth

A numeric that scales the width of the cis-effect edges.

geWidth

A numeric that scales the width of the gene expression nodes.

cnWidth

A numeric that scales the width of the DNA copy number nodes.

circleDist

A numeric that scales the inner and outer circle.

gNames

A character containing the gene names to written inside the nodes.

main

The character to be plotted as plot title.

remove

A logical indicating whether to remove genes without trans-effects.

Author(s)

Wessel N. van Wieringen: [email protected]

References

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

See also pathway1sample.

Examples

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# 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)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: mvtnorm
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sigaR documentation built on May 6, 2019, 3:40 a.m.