geom_strip: geom_strip

In GuangchuangYu/ggtree: an R package for visualization of tree and annotation data

geom_strip

Description

annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label

Usage

geom_strip(
  taxa1,
  taxa2,
  label,
  offset = 0,
  offset.text = 0,
  align = TRUE,
  barsize = 0.5,
  extend = 0,
  fontsize = 3.88,
  angle = 0,
  geom = "text",
  hjust = 0,
  color = "black",
  fill = NA,
  family = "sans",
  parse = FALSE,
  ...
)

Arguments

taxa1	taxa1
taxa2	taxa2
label	add label alongside the bar (optional)
offset	offset of bar and text from the clade
offset.text	offset of text from bar
align	logical, whether to align bars to the most distant bar ,defaults to "TRUE" Note that if "FALSE", the bars might cross the tree
barsize	set size of the bar
extend	extend bar length vertically
fontsize	set size of the text
angle	set the angle of text
geom	one of 'text' or 'label'
hjust	adjust the horizonal position of the bar
color	set color for bar and label
fill	set color to fill label background, only work with geom='label'
family	"sans" by default, can be any supported font
parse	logical, whether to parse labels, if "TRUE", the labels will be parsed into expressions, defaults to "FALSE"
...	additional parameter

Value

ggplot layers

Author(s)

Guangchuang Yu

References

For more detailed demonstration of this function, please refer to chapter 5.2.1 of Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.

Examples

library(ggtree)
tr<- rtree(15)
x <- ggtree(tr)
x + geom_strip(13, 1, color = "red") + geom_strip(3, 7, color = "blue")

GuangchuangYu/ggtree documentation built on Oct. 31, 2024, 10:10 a.m.