Data visualization of frequencies of state transitions (possibly in R?)
How about a Sankey diagram with time on the x-axis and flow width representing state transition frequency. Here is a SO discussion on implementing Sankey diagrams in R.


One possible R package is {riverplot}... here is code showing the first transition in your data:

library(riverplot)
nodes &lt;- as.character(sapply(1:2, FUN = function(n){paste0(LETTERS[1:3],n)}))
edges &lt;- list(A1=list(C2=4), B1=list(A2=1,C2=1,B2=2), C1=list(C2=2))
r &lt;- makeRiver( nodes, edges, node_xpos= c( 1,1,1 ,2,2,2),
                node_labels= c( A1= "A", B1= "B", C1= "C", A2="A",B2="B",C2="C" ))
plot( r )


Will produce this: