Plot a life cycle diagram from a matrix population model

Plots the life cycle diagram illustrated by a matrix population model. This function processes the matrix model and passes the information to the graphViz function in DiagrammeR. See https://rich-iannone.github.io/DiagrammeR/.

plot_life_cycle(
  matA,
  stages,
  title = NULL,
  shape = "egg",
  fontsize = 10,
  nodefontsize = 12,
  edgecol = "grey",
  node_order = NULL
)

Arguments

matA: A matrix population model (i.e., a square projection matrix)
stages: Optional vector of stage class labels. If missing, it first attempts to infer them from dimnames(matA). If these are also NULL, then reverts to integers 1:ncol(A).
title: Optional title for the plot. Defaults to NULL.
shape: The shape to be used for the stages of the diagram. Any node shape accepted by graphViz is acceptable.
fontsize: Size of the font used in the diagram.
nodefontsize: Size of the font used in the node part of the diagram.
edgecol: Colour of the arrows in the diagram.
node_order: An optional numeric vector giving the order that the nodes should be presented in the plot. Default is `NULL` whereby the order is the same as `stages`, or row/column names, of the matrix.

Value

An object of class grViz representing the life cycle diagram

Author

Owen R. Jones <jones@biology.sdu.dk>

Examples

matA <- rbind(
  c(0.1, 0, 0, 0, 1.4),
  c(0.5, 0.2, 0, 0, 0),
  c(0, 0.3, 0.3, 0, 0),
  c(0, 0, 0.4, 0.4, 0.1),
  c(0, 0, 0, 0.1, 0.4)
)

plot_life_cycle(matA)


# One could save the diagram as a PNG file using a combination of `export_svg`
# (from the `DiagrammeRsvg` package) and `rsvg_png` (from the `rsvg` package)
# like this:
if (FALSE) { # \dontrun{
p1 <- plot_life_cycle(matA)
p1 %>%
  DiagrammeRsvg::export_svg %>%
  charToRaw() %>%
  rsvg::rsvg_png("my life cycle.png")
} # }

# Change the order of the nodes and give them names
plot_life_cycle(matA,
  stages = c("A", "B", "C", "D", "E"),
  node_order = 5:1
)