annotate_balance: annotate_balance

Description Usage Arguments Value Author(s) References Examples

View source: R/plot_utils.R

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

1
2
3
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

1
2
3
4
5
6
7
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)

jsilve24/philr documentation built on April 3, 2020, 7:30 a.m.