unrooted tree layout — layout_tree_unrooted • graphlayouts

arranges the nodes of a tree (or forest) in the plane without a designated root, using algorithms developed for drawing phylogenies.

Usage

layout_as_tree_unrooted(
  g,
  mode = c("equalangle", "equaldaylight", "stress"),
  weights = NA,
  daylight_iter = 15,
  iter = 500,
  tol = 1e-04,
  bbox = 30
)

layout_igraph_tree_unrooted(
  g,
  mode = c("equalangle", "equaldaylight", "stress"),
  weights = NA,
  daylight_iter = 15,
  iter = 500,
  tol = 1e-04,
  bbox = 30,
  circular
)

Arguments

g: igraph object. Each connected component must be a tree (acyclic).
mode: which algorithm to use. One of "equalangle" (default), "equaldaylight" or "stress". See details.
weights: possibly a numeric vector with edge weights, interpreted as branch lengths. If this is NULL and the graph has a weight edge attribute, then the attribute is used. If this is NA then unit branch lengths are used (even if the graph has a weight attribute). By default, unit branch lengths are used.
daylight_iter: number of refinement sweeps for mode = "equaldaylight".
iter: number of iterations during stress optimization (only used for mode = "stress").
tol: stopping criterion for stress optimization (only used for mode = "stress").
bbox: width of layout. Only relevant to determine the placement of disconnected components (forests).
circular: not used

Value

matrix of xy coordinates

Details

Three algorithms are available:

"equalangle" (Felsenstein, 1989): each subtree is allotted an angular wedge proportional to its number of leaves. Linear time, but can look crowded on unbalanced trees.
"equaldaylight" (Felsenstein): iteratively equalizes the angular gaps ("daylight") around each internal node, starting from the equal-angle layout, for a more balanced drawing.
"stress": stress majorization using the patristic (tree path-length) distances as target distances, reusing the package's stress engine.

Branch lengths (edge weights) are respected when present; otherwise unit lengths are used.

The layout_igraph_* function should not be used directly. It is only used as an argument for plotting with 'igraph'. 'ggraph' natively supports the layout.

References

Felsenstein, J. (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.

Bachmaier, C., Brandes, U., & Schlieper, B. (2005). Drawing phylogenetic trees. In International Symposium on Algorithms and Computation (pp. 1110-1121). Springer, Berlin, Heidelberg.

Examples

library(igraph)
g <- make_tree(20, 3, mode = "undirected")

xy <- layout_as_tree_unrooted(g)
xy <- layout_as_tree_unrooted(g, mode = "equaldaylight")