pf.tree: ggtree-based plotting of phylofactor bins or factors

In reptalex/phylofactor: phylofactor

ggtree-based plotting of phylofactor bins or factors

Description

ggtree-based plotting of phylofactor bins or factors

Usage

pf.tree(pf, tree = NULL, method = "factors", factors = NULL,
  ignore.tips = TRUE, groups = NULL, colors = NULL,
  GroupList = NULL, bg.color = NA, bg.alpha = 0.1, alphas = NULL,
  layout = "circular", rootnode = FALSE, top.layer = F,
  top.alpha = 0.1, color.fcn = viridis::viridis, ...)

Arguments

pf	phylofactor class object
tree	An alternative tree on which to plot the phylogenetic factors pf$tree.
method	either "factors" or "bins", based on whether to use factors ( factors along with groups) or resultant bins (pf$bins) from phylofactorization.
factors	vector of factor numbers to be plotted
groups	vector of groups (1 or 2) to be plotted for each factor. Default is 1
colors	colors for each factors x groups pair, or each member of GroupList
GroupList	optional list of groups for plotting
bg.color	background color
bg.alpha	background alpha
alphas	vector, of length = nrow(factor.map) or length(GroupList) or, if default settings, of length pf$nfactors. Controls alphas for highlights of each clade. Warning: the current output legend gives you the colors layered onto each clade. Layering transparent colors on top of one-another will produce a different color not in the legend..
layout	See ggtree. Default is "circular"
rootnode	Logical. If true, will fill in the root node. Default controls root only with bg.color
top.layer	Logical. If true, will superimpose hilights on top of tree. If false, tree will layer on top of hilights.
top.alpha	Numeric. Alpha value for top.layer
color.fcn	Color function for plotting. Default is viridis.
...	optional arguments for ggtree

Examples

library(phylofactor)
data(FTmicrobiome)
pf <- FTmicrobiome$PF
big.tree <- FTmicrobiome$tree
tax <- FTmicrobiome$taxonomy
gg <- pf.tree(pf,factors=1:3,layout='circular')
gg$ggplot
gg$legend

## We can also focus on a universal tree
# pf.tree(pf,big.tree,factors=1:3)

## and a sub-tree
bacteroidetes <- tax$OTU_ID[grepl('p__Bacteroidetes',tax$taxonomy)] %>%
 intersect(pf$tree$tip.label)
bacteroidetes.tree <- drop.tip(big.tree,setdiff(big.tree$tip.label,bacteroidetes))
pf.tree(pf,bacteroidetes.tree,factors=setdiff(1:pf$nfactors,41))
## factor 41 contains a large, paraphyletic group that encompases all of the 
## bacteroidetes - this will color our entire tree purple.

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.