Export the transition graph as Graphviz DOT or Mermaid text

toDot writes the transition graph of a Markov chain in the DOT language of Graphviz; toMermaid writes it as a Mermaid flowchart. The states are the nodes and every transition with positive probability is an edge labelled with its probability.

Usage

toDot(object, file = NULL, digits = 3, minProbability = 0, direction = "LR")

# S4 method for class 'markovchain'
toDot(object, file = NULL, digits = 3, minProbability = 0, direction = "LR")

toMermaid(
  object,
  file = NULL,
  digits = 3,
  minProbability = 0,
  direction = "LR"
)

# S4 method for class 'markovchain'
toMermaid(
  object,
  file = NULL,
  digits = 3,
  minProbability = 0,
  direction = "LR"
)

Arguments

object: A markovchain object.
file: An optional file path. If given, the text is also written there (UTF-8) and returned invisibly.
digits: The number of significant digits of the probabilities shown on the edges.
minProbability: Transitions with probability not above this value are left out; the default, 0, keeps every possible transition.
direction: The layout direction: "LR" (left to right, the default), "TB" (top to bottom), "RL" or "BT".

Value

The text, as a single character string (invisibly when file is given).

Details

The edges follow the outgoing distribution of each state whatever the storage of the transition matrix (byrow), so a chain and its column-stochastic copy give the same text. State names are quoted and escaped, so they may contain spaces, quotes or other punctuation. In the Mermaid output the nodes get the identifiers s1, s2, ..., with the state names as labels, because Mermaid identifiers cannot contain arbitrary characters.

The DOT text can be rendered with Graphviz (for instance dot -Tpng chain.dot -o chain.png) or with DiagrammeR::grViz(); the Mermaid text can be pasted into any Markdown renderer that supports Mermaid diagrams, or rendered with DiagrammeR::mermaid().

Examples

statesNames <- c("a", "b", "c")
mc <- new("markovchain", states = statesNames, name = "Example",
  transitionMatrix = matrix(c(0.5, 0.5, 0, 0.2, 0.3, 0.5, 0, 0, 1),
    byrow = TRUE, nrow = 3, dimnames = list(statesNames, statesNames)))
cat(toDot(mc), "\n")
#> digraph "Example" {
#>   rankdir=LR;
#>   node [shape=circle];
#>   "a";
#>   "b";
#>   "c";
#>   "a" -> "a" [label="0.5"];
#>   "a" -> "b" [label="0.5"];
#>   "b" -> "a" [label="0.2"];
#>   "b" -> "b" [label="0.3"];
#>   "b" -> "c" [label="0.5"];
#>   "c" -> "c" [label="1"];
#> } 
cat(toMermaid(mc, direction = "TB"), "\n")
#> flowchart TB
#>   s1(("a"))
#>   s2(("b"))
#>   s3(("c"))
#>   s1 -->|"0.5"| s1
#>   s1 -->|"0.5"| s2
#>   s2 -->|"0.2"| s1
#>   s2 -->|"0.3"| s2
#>   s2 -->|"0.5"| s3
#>   s3 -->|"1"| s3