R markov chain package, is possible to set the coordinates and size of the nodes?

问题

I'm working with R in some biology-behavioural problems, and I have a transition matrix which I want to plot in a certain way.

I'm using the markovchain package, which makes easy the visualization.

This is a test-code and it's output.

> a<-array(0.25,dim = c(4,4))
> markov<-new("markovchain",transitionMatrix=a,states=c("a","b","c","d"), name="test")
> markov
test 
 A  4 - dimensional discrete Markov Chain defined by the following states: 
 a, b, c, d 
 The transition matrix  (by rows)  is defined as follows: 
 a    b    c    d
 a 0.25 0.25 0.25 0.25
 b 0.25 0.25 0.25 0.25
 c 0.25 0.25 0.25 0.25
 d 0.25 0.25 0.25 0.25

 > plot(markov)

The thing is, I would like to set the coordinates of the graph nodes to place them in a 2D grid or something like that, and also to set the size of the nodes. I know that this package works with S4, but I'm not really familiar with it and don't know if there are any arguments that would be useful to me. Any help?

回答1:

You could do this:

layout <- matrix(c(0,0,0,1,1,1,1,0), ncol = 2, byrow = TRUE)

     # [,1] [,2]
# [1,]    0    0
# [2,]    0    1
# [3,]    1    1
# [4,]    1    0

plot(markov, vertex.size = 25, layout = layout)

The layout is a matrix of two columns. Each row contains coordinates per node. With vertex.size, you can adjust the size of the nodes. Note that markovchain package benefits from the igraph package to do so.

With these layouts

layout <- matrix(c(4,-2,7,2,8,8,8,-4), ncol = 2, byrow = TRUE)
     # [,1] [,2]
# [1,]    4   -2
# [2,]    7    2
# [3,]    8    8
# [4,]    8   -4

plot(markov, vertex.size = 25, layout = layout)

You would have this:

来源：https://stackoverflow.com/questions/43205378/r-markov-chain-package-is-possible-to-set-the-coordinates-and-size-of-the-nodes

标签

plot

chain

markov