Plot a life cycle diagram from a matrix population model

Source: R/plot_life_cycle.R

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/. Transitions with value 0 are assumed to be biologically impossible, and arrows are omitted from the diagram. Transition rates of NA are shown as arrows, labelled with NA.

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)



# Plot and label unknown transitions as NA
matA_na <- matA
matA_na[1, 5] <- NA
plot_life_cycle(matA_na)



# 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
)