clonevol (version 0.99.11)

plot.tree.clone.as.branch: Plot a consensus tree using branch-based visualization

Description

Plot a consenus clonal evolution tree where clones are visualized as branch leading to a node

Usage

# S3 method for tree.clone.as.branch
plot(mt, angle = 15, branch.width = 1,
  branch.text.size = 0.3, node.size = 3, node.label.size = 0.75,
  node.text.size = 0.5, event.sep.char = ",", show.event = TRUE,
  tree.rotation = 0, text.angle = NULL, tree.label = NULL,
  branch.border.width = NULL, ...)

Arguments

branch.text.size

Text size of events mapped on branches (default=0.3)

node.size

Tree node size (default=3)

node.label.size

Text size of node label (default=0.75)

node.text.size

Text size of the node annotation (eg. sample names) (default=0.5)

event.sep.char

Character used to separate events when multiple events are mapped onto a branch (default=',')

show.event

Show event? (default=TRUE)

tree.rotation

Angle (degrees) to rotate the tree in output plot (default=0, meaning tree is plotted top-down)

text.angle

Angle of text, when tree is rotated, user should change this accordingly (default=NULL)

tree.label

Label of the tree (default=NULL)

branch.border.width

Width of the border of the branch (default=NULL)

mt:

a consensus tree. If y is output of infer.clonal.models, consensus trees are stored in y$matched$mereged.trees, eg. y$matched$mereged.trees[[1]] gives the first tree, and so on.

angle:

the angle to draw branch outward from the center (default = 15 degrees). Lower value makes trees tighter.

branch.width:

The width of the tree branch, default = 1

Examples

# NOT RUN {
library(clonevol)
data(aml1)
tree = aml1$matched$merged.trees[[1]]
\dontrun{
plot.tree.clone.as.branch(tree)
}
# }