plottree: Display merger tree

In obreschkow/mergertrees: Handle astrophysicsal merger trees

Description

Visualise rooted directional trees, such as the merger trees of halos and galaxies.

Usage

plottree(
  tree = NULL,
  normalize.mass = TRUE,
  sort = TRUE,
  spacetype = 3,
  straightening = 0,
  simplify = FALSE,
  style = 3,
  circle.height = 0,
  root.length = 0.5,
  leaf.length = 0.5,
  margin = 0.03,
  col = rainbow(100, start = 0, end = 5/6),
  draw.edges = TRUE,
  draw.vertices = FALSE,
  draw.box = TRUE,
  add = FALSE,
  xlim = c(0, 1),
  ylim = c(0, 1),
  scale = 1,
  gamma = 1,
  min = 0,
  vertex.size = 1,
  pdf.filename = NULL,
  pdf.size = 5,
  forced.x = NULL,
  forced.y = NULL,
  overlap = 0.001
)

Arguments

tree	list of vectors of equal lengths (n), specifying the n vertices (halos) a tree. These vectors are: descendant (mandatory) specifies a descendant index for each vertex. This vector must contain one zero, which specifies the root vertex. All other values must be positive integers. mass (optional) specifies contains the masses of the vertices. If not given, the mass will be chosen equal to the number of leaves in the subtree leading to this node. value (optional) contains values, normalized to [0,1], to be displayed in colour. length (optional) number of vertical steps ("snapshots") to the descendant of each vertex. If not given, the default values is one.
normalize.mass	logical flag specifying whether the masses should be normalized to the root mass
sort	logical flag, specifying if the branches are ordered such that higher mass branches are more central
spacetype	integer, specifying how much horizontal space is allocated to each progenitor branch: 1=all progenitors get equal space, 2=proportional to number of leaves, 3=proportional to mass
straightening	real between 0 and 1 specifying the maximal mass-ratio up to which it is enforced that the main progenitor is strictly vertically above its descendant.
simplify	logical flag. If TRUE, all the vertices, other than the root, with only one progenitor are removed for graphical simplicity.
style	integer value to specify the rendering: 1=straight lines, 2=splines, 3=polygon splines with optimal vertex-matching
circle.height	real between 0 and 1 specifying the relative vertical height of circles drawn at the nodes (only with style=3)
root.length	length of the root branch, extending down from the root halo
leaf.length	length of the leaf branches, extending up from the leaves
margin	thickness of margin surrounding the plot
col	colour of the edges; or a vector of colours if values have been specified in the tree
draw.edges	logical flag to turn on/off edges
draw.vertices	logical flag to turn on/off vertices
draw.box	logical flag to turn on/off a black frame around the box
add	logical flag specifying whether the plot should be added to an existing plot
xlim	horizontal range of the tree with margin (only needed if add = TRUE)
ylim	vertical range of the tree with margin (only needed if add = TRUE)
scale	scaling factor to convert masses into line widths
gamma	scaling exponent to convert masses into line widths
min	minimum linewidth
vertex.size	scaling factor of the vertex size
pdf.filename	optional file name of a PDF file to be saved
pdf.size	optional size of the PDF image
forced.x	optional vector allowing the user to enforce the x-positions of individual nodes. Use NAs for automatic values.
forced.y	optional vector allowing the user to enforce the y-positions of individual nodes. Use NAs for automatic values.
overlap	optional number specifying a small vertical overlap between branches to avoid spurious gaps in graphical outputs

Author(s)

Danail Obreschkow

See Also

buildtree

Examples

## plot default tree
plottree()

## show a simple custom tree
tree = list(mass = c(1,0.6,0.1,0.5,0.4), descendant = c(0,1,2,2,1))
plottree(tree)

obreschkow/mergertrees documentation built on June 25, 2021, 6:40 p.m.