annotate_balance: annotate_balance

In philr: Phylogenetic partitioning based ILR transform for metagenomics data

Description

annotate a balance oriented with respect to the PhILR transform. That is, you can specify labels for the numerator (up) and denominator (down).

Usage

annotate_balance(tr, coord, p = NULL, labels = c("+", "-"),
  offset = 0, offset.text = 0.03, bar = TRUE, barsize = 0.01,
  barfill = "darkgrey", geom = "text", ...)

Arguments

tr	phylo object
coord	named internal node/balance to annotate
p	ggtree plot (tree layer), if NULL then a new plot will be created.
labels	label for the numerator and denominator of the balance respectively
offset	offset for bar (if bar=TRUE) from tips
offset.text	offset of text from bar (if bar=TRUE) or from tips (if bar=FALSE)
bar	logical, should bar for each clade be plotted
barsize	width of bar (if bar=TRUE)
barfill	fill of bar
geom	geom used to draw label (e.g., 'text' or 'label')
...	additional parameters passed to geom_rect and specified geom

Value

ggplot object

Author(s)

Justin Silverman

References

Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628

Examples

tr <- named_rtree(10)

annotate_balance(tr, 'n4', size=7)
annotate_balance(tr, 'n4', size=7, barsize=0.04, barfill='darkgreen', offset.text=0.05, color='red')
annotate_balance(tr, 'n4', bar=FALSE, size=7)
annotate_balance(tr, 'n4', bar=TRUE, size=7, labels=c('Num', 'Denom'), offset.text=.3)
annotate_balance(tr, 'n4', bar=TRUE, geom='label', size=8, offset.text=0.1)

Example output

philr documentation built on Nov. 8, 2020, 5:38 p.m.