graphical.node.patterns: Define graphical parameters to plot phylogenetic tree.

In vanderleidebastiani/daee: Data Analysis for Ecology and Evolution

Description

Function to define graphical parameters to each edge when draw a phylogenetic tree. See details.

Usage

graphical.node.patterns(
  tree,
  nodes,
  basicpattern,
  nodespatterns,
  include.node = TRUE,
  force.order = TRUE
)

Arguments

tree	phylogeny as an object of class "phylo".
nodes	a vector with node label to search the edges to change the basic graphical parameter.
basicpattern	the basic pattern for graphical parameter. This is apply for all edges.
nodespatterns	a vector with new graphical parameter for each node label. This change the basic graphical parameter in each node.
include.node	logical argument (TRUE or FALSE) to specify if edge of each node is include in change (default include.node = TRUE).
force.order	logical argument (TRUE or FALSE) to specify if force the search as according to edges (default force.order = TRUE).

Details

This function can be used to especify diferent graphical parameters (e.g. color, width and line types) for specific nodes when draw a phylogenetic tree. First, the basicpattern argument is defined for all edges of phylogenetic tree and when the basic pattern is changed in all edge within of each node, following the nodespatterns specify. The argument force.order specify if changes following order in nodes arguments step by step (this case, some changes may have no effect) or change are done from root to tips.

Value

A vector with the new graphical parameters for each edge in phylogenetic tree.

Author(s)

Vanderlei Julio Debastiani <[e-mail]>

See Also

plot.phylo plotcollapse.phylo

Examples

set.seed(10)
tree <- rtree(15)
tree <- makeNodeLabel(tree)
plot.phylo(tree, show.node.label = TRUE)

edge.col <- graphical.node.patterns(tree, nodes = c("Node2", "Node8"),
   basicpattern = "black", nodespatterns = c("red","blue"))
edge.col # Color vector for each edge
plot.phylo(tree, show.node.label = TRUE, edge.color = edge.col)

edge.width <- graphical.node.patterns(tree, nodes = c("Node11","Node3"), 
   basicpattern = 1, nodespatterns = 5, include.node = FALSE)
edge.width # width vector for each edge
plot.phylo(tree, show.node.label = TRUE, edge.width = edge.width)

tree <- rtree(250)
tree <- makeNodeLabel(tree)
plot(tree, show.tip.label = FALSE)
edge.col <- graphical.node.patterns(tree, nodes = tree$node.label, 
   basicpattern = "black", nodespatterns = rainbow(length(tree$node.label)))
edge.col
plot.phylo(tree, edge.color = edge.col, show.tip.label = FALSE)

vanderleidebastiani/daee documentation built on Jan. 22, 2021, 2:41 p.m.