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

Description Usage Arguments Details Value Author(s) References See Also Examples

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

plotdetailed(phi, weights = NULL, main = "", stimuli = NULL,
  node.color = "grey", node.size1 = 30, node.size2 = 7, edge.width = 1, 
  edge.arrowsize = 0.5, layout = layout.circle, pdf = NULL, pointsize = 12, 
  edge.width.inhib = 1.5, plot.legend = TRUE,
  label.cex = 1, vlabel.cex = 0.6, tk = FALSE, fontsize=20, rescale=TRUE)

layout.ellipsis(ig, a=1, b=1.5)

`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.

`fontsize`	Deprecated. Still there for compatibility issues with `plotdetailed_Rgraphviz`. Use `cex.label` to control edge label size.
`node.color`	Define coloring of nodes.
`node.size1`	Width of a rectangular node.
`node.size2`	Height of a rectangular node.
`edge.width`	Width of edges.
`edge.arrowsize`	Size of edge ends.
`layout`	Graph layout algorithm or matrix with node coordinates.
`pdf`	Pdf output file name.
`pointsize`	Pointsize argument used in pdf device.
`edge.width.inhib`	Width of inhibitory edges.
`plot.legend`	Define if legend should be drawn or not.
`label.cex`	Edge label size factor.
`vlabel.cex`	Node label size factor.
`tk`	Use tk-plotting engine or not.
`rescale`	Rescaling coordinates or not.
`ig`	Igraph object.
`a`	Semi major axis of ellipse.
`b`	Semi minor axis of ellipse.

Plot a graph encoded in adjacency matrix phi using the igraph library. Activation edges are drawn as solid lines, inhibition edges as dashed lines. Stimuli nodes can be colored red using the stimuli argument.

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.

layout.ellipsis is another graph layout making elliptical graphs possible. Can be used as layout argument for plotting. Use rescale=FALSE if using layout.ellipsis.

A list object holding the igraph object ig and the layout coordinates layout:

`ig`	Igraph object created from the adjacency matrix.
`layout`	Matrix with two columns, holding the x and y coordinates of the elements in the graph.

Christian Bender

none

plotdetailed_Rgraphviz

## 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]))
diag(mat) <- 0
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(mat,weights,"Some random graph",stimuli,layout=layout.graphopt)
layoutmat <- cbind(c(1,2,3,4,5), c(5,4,3,2,1))
plotdetailed(mat,weights,"Some random graph",stimuli,layout=layoutmat)

## End(Not run)