plotdetailed_Rgraphviz: plotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail

In ddepn: Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

Description

plotdetailed_Rgraphviz uses Rgraphviz to plot a graph containing activations and inhibitions. Input is an adjacency matrix with activation edge represented by a 1, inhibition by a 2.

Usage

plotdetailed_Rgraphviz(phi,weights=NULL,main="",stimuli=NULL,
			layoutType = "dot", fontsize=20)
get.labels(phi)
get.arrowhead(phi)
get.arrowtail(phi)

Arguments

phi	Adjacency matrix. The network to be plotted.
weights	Optional matrix of edge weights.
main	Optional character string containing main title for the plot.
stimuli	List of input stimuli. Are marked as red filled nodes in the plot.
layoutType	The graphviz layout for drawing the network.
fontsize	Fontsize of text in the plot.

Details

get.labels, get.arrowhead and get.arrowtail are helper functions for the plot construction and usually not called directly.

The stimuli list describes the input stimuli or inhibitions. Each of these external treatment nodes are drawn as red nodes in the graph. The format of the list should be:\ Example: Assume two treatments EGF and X, a data matrix data:

	EGF_1	EGF_1	EGF_2	EGF_2	EGF&X_1	EGF&X_2	EGF&X_2	EGF&X_2
EGF	0	0	0	0	0	0	0	0
X	0	0	0	0	0	0	0	0
AKT	1.45	1.8	0.99	1.6	1.78	1.8	1.56	1.58

The stimuli list should be in the format: stimuli <- list(c(EGF=1),c(EGF=1,X=2)), i.e. each element in the list corresponds to a treatment. Each treatment is a named numeric vector describing the row indices of the treatments in the data matrices.

Value

none

Author(s)

Christian Bender

Examples

## Not run: 
library(ddepn)
mat <- matrix(sample(c(0,1,2),25,replace=TRUE), nrow=5,ncol=5, 
	dimnames=list(LETTERS[1:5],LETTERS[1:5]))
weights <- matrix(sample(c(1:25),25,replace=TRUE), nrow=5,ncol=5, 
	dimnames=list(LETTERS[1:5],LETTERS[1:5]))
stimuli <- list(list(A=1))
plotdetailed_Rgraphviz(mat,weights,"Some random graph",stimuli,layoutType="dot")
plotdetailed_Rgraphviz(mat,weights,"Some random graph",stimuli,layoutType="neato")

## End(Not run)

ddepn documentation built on May 2, 2019, 4:42 p.m.