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
|
# Custom print function for class AttractorInfo
print.AttractorInfo <- function(x, activeOnly = FALSE, ...)
{
numGenes <- length(x$stateInfo$genes)
attractors <- x$attractors
for (i in seq_along(attractors))
{
if (is.null(attractors[[i]]$initialStates))
# simple attractor
{
printSynchronousAttractor(getAttractorSequence(x, i), i,
attractors[[i]]$basinSize, activeOnly=activeOnly)
}
else
{
# print general information on the attractor
cat("Attractor ",i," is a complex/loose attractor consisting of ",ncol(attractors[[i]]$involvedStates),
" state(s) and ",ncol(attractors[[i]]$initialStates), " transition(s)",sep="")
if (activeOnly)
{
cat(".\nActive genes in the state transitions: \n")
initialStates <- t(apply(attractors[[i]]$initialStates,2,function(state)
dec2bin(state,numGenes)))
nextStates <- t(apply(attractors[[i]]$nextStates,2,function(state)
dec2bin(state,numGenes)))
binMatrix <- data.frame(initialStates,nextStates)
apply(binMatrix,1,function(row)
{
state1 <- paste(x$stateInfo$genes[which(row[seq_len(numGenes)] == 1)],collapse=", ")
if (state1 == "")
state1 <- "--"
state2 <- paste(x$stateInfo$genes[which(row[seq_len(numGenes) + numGenes] == 1)],collapse=", ")
if (state2 == "")
state2 <- "--"
cat(state1," => ",state2,"\n",sep="")
})
}
else
{
cat(":\n\n")
initialStates <- apply(attractors[[i]]$initialStates,2,function(state)
paste(dec2bin(state,numGenes),collapse=""))
nextStates <- apply(attractors[[i]]$nextStates,2,function(state)
paste(dec2bin(state,numGenes),collapse=""))
binMatrix <- data.frame(initialStates,nextStates)
apply(binMatrix,1,function(row)
{
cat(row[1]," => ",row[2],"\n",sep="")
})
cat("\nGenes are encoded in the following order: ",paste(x$stateInfo$genes,collapse=" "),"\n\n",sep="")
}
}
}
return(invisible(x))
}
|
