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
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
# Plot a wiring graph of the network <network> with the supplied
# graphical parameters.
# Requires igraph.
# Returns the igraph structure representing the wiring graph.
plotNetworkWiring <- function(network,layout=layout.fruchterman.reingold,plotIt=TRUE,...)
{
stopifnot(inherits(network,"ProbabilisticBooleanNetwork") | inherits(network,"BooleanNetworkCollection")
| inherits(network,"BooleanNetwork") | inherits(network,"SymbolicBooleanNetwork"))
if (installed.packages()["igraph","Version"] < package_version("0.6"))
bias <- 1
else
bias <- 0
edgeList <- c()
# construct list of edges from interactions
if (inherits(network,"BooleanNetwork"))
# deterministic network
{
for (i in seq_along(network$genes))
{
if (network$interactions[[i]]$input[1] != 0)
# no edges for constant genes
{
edgeList <- rbind(edgeList,
cbind(network$interactions[[i]]$input,
rep(i,length(network$interactions[[i]]$input))))
}
}
}
else
if (inherits(network,"SymbolicBooleanNetwork"))
# symbolic network
{
inputs <- lapply(network$interactions, getInputs, index=TRUE)
for (i in seq_along(network$genes))
{
edgeList <- rbind(edgeList,
cbind(inputs[[i]],
rep(i,length(inputs[[i]]))))
}
}
else
# probabilistic network
{
for (i in seq_along(network$genes))
{
for (j in seq_along(network$interactions[[i]]))
{
if (network$interactions[[i]][[j]]$input[1] != 0)
# no edges for constant genes
{
edgeList <- rbind(edgeList,
cbind(network$interactions[[i]][[j]]$input,
rep(i,length(network$interactions[[i]][[j]]$input))))
}
}
}
}
# build graph from edge list
res <- graph.data.frame(edgeList-bias,directed=TRUE,vertices=as.data.frame((seq_along(network$genes)) - bias))
res <- set.vertex.attribute(res,"name",value=network$genes)
args <- list(...)
# check for certain graphical parameters in ...
# that have different default values in this plot
if (is.null(args$vertex.color))
args$vertex.color <- "grey"
if (is.null(args$edge.arrow.size))
args$edge.arrow.size <- 0.5
if (is.null(args$vertex.label.cex))
args$vertex.label.cex <- 0.7
if (is.null(args$vertex.size))
args$vertex.size <- 18
if (plotIt)
{
plot(res,vertex.label=network$genes,vertex.label.cex=args$vertex.label.cex,
vertex.size=args$vertex.size,vertex.color=args$vertex.color,
edge.arrow.size=args$edge.arrow.size,
layout=layout,...)
}
return(invisible(res))
}
|
