Plot a tree representing the clonal structure of a sample Return the graph object (with node name prefixed with node.prefix.to.add)
# S3 method for tree
plot(v, node.shape = "circle", display = "tree",
node.size = 50, node.colors = NULL, color.node.by.sample.group = FALSE,
color.border.by.sample.group = TRUE, show.legend = TRUE,
tree.node.text.size = 1, cell.frac.ci = TRUE, node.prefix.to.add = NULL,
title = "", node.annotation = "clone",
node.label.split.character = NULL, node.num.samples.per.line = NULL,
out.prefix = NULL, graphml.out = FALSE, out.format = "graphml")clonal structure data frame as the output of enumerate.clones
tree or graph
show sample names in node
c('clone', 'sample.with.cell.frac.ci', 'sample.with.nonzero.cell.frac.ci', 'sample.with.cell.frac.ci', 'sample.with.cell.frac.ci.founding.and.subclone') Labeling mode for tree node. 'sample.with.cell.frac.ci' = all samples where clone's signature mutations detected togeter with cell.frac.ci if cell.frac.ci=T; 'sample.nonzero.cell.frac' = samples where clones detected with nonzero cell fraction determined by subclonal.test 'sample.with.cell.frac.ci.founding.and.subclone': show all execpt samples where cell frac is zero and not subclone if cell.frac is diff from zero; default = 'clone' = only clone label is shown 'sample.term.clone' = samples where clones are terminal clones (ie. clones that do not have subclones in that sample)
replace this character by "\n" to allow multi line labeling for node; esp. helpful with multi samples sharing a node being plotted.
named vector of colors to plot for nodes, names = clone/cluster labels; if NULL (default), then use v$color
if TRUE, and if column sample.group and sample.group.color exists, then color node by these; also add legend
if TRUE, color border of clones in tree or bell plot based on sample grouping
show sample group legends, etc.