clonevol (version 0.99.11)

convert.consensus.tree.clone.to.branch: Create trees for all merged.trees in clonevol output

Description

Take all merged/concensus trees in clonal evolution object output of infer.clonal.models function, and convert them to branch-based clonal evolution tree by adding additional columns and branch length scale, => make them ready to plot.

Usage

convert.consensus.tree.clone.to.branch(x, cluster.col = "cluster",
  branch.scale = "none")

Arguments

x:

output of infer.clonal.models

cluster.col:

cluster column name (used to count variants in each cluster/clone, and scale tree branch length

branch.scale:

values=c('none', 'sqrt', 'log2'), scale branch length by corresponding transformations. Note, branch length will be estimated by the number of variants in each cluster/clone

Examples

# NOT RUN {
data(aml1)
y = aml1
y <- convert.consensus.tree.clone.to.branch(y, branch.scale = 'sqrt')

# }