chromatophylo: Plot tree through time with coloured edges
In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description Usage Arguments Details Examples

Return a geom_object() of a phylogenetic tree through time. Requires tree given to be rooted, time callibrated and bifurcating.

1 2	chromatophylo(tree, edge.cols = NULL, edge.sizes = NULL, legend.title = "", reduce.overlap = TRUE)

`edge.cols`	data.frame of values used to colour edges (see example)
`edge.sizes`	data.frame of sizes used to determine the size of edges
`legend.title`	text for legend if edge.cols provided
`reduce.overlap`	boolean, TRUE will prevent edges from overlapping in plot, may take longer to plot

No details – see details.

# Quick example without colours
tree <- rtree (50)  # random tree with fossils
plot (tree)  # ape plot
chromatophylo (tree)  # chromatophylo


# Example with collapseTips() + calcEdgeDiversity()
# generate random tree
tree <- rtree (100)
# add edge labels to track edges after collapse
tree$edge.label <- paste0 ('edge_', 1:nrow (tree$edge))
# generate edge diversity using two intervals
ed <- calcEdgeDiversity (tree, n.intervals=2)
# iteratively drop all tip edges with > 10% tree age
tree.age <- getSize (tree, 'rtt')
ctree <- collapseTips (tree, min.length=tree.age*0.1, iterative=TRUE)
# reconstruct edge diversity data frame without dropped edges
new.ed <- data.frame (edge.label=ctree$edge.label)
new.ed$edge <- 1:nrow (new.ed)
match.counts <- match (ctree$edge.label, ed$edge.label)
new.ed$count <- ed$count[match.counts]
# convert count to logged Z-score for maximum colour separation
new.ed$col <- (log (new.ed$count) - mean (log (new.ed$count))) /
  sd (log (new.ed$count))
ed$col <- (log (ed$count) - mean (log (ed$count))) /
  sd (log (ed$count))
# plot before
chromatophylo (tree, edge.cols=ed, legend.title='Diversity') + ggtitle ('Before collapse')
# plot after
chromatophylo (ctree, edge.cols=new.ed, legend.title='Diversity') + ggtitle ('After collapse')