collapse: collapse-ggtree

In YuLab-SMU/ggtree: an R package for visualization of tree and annotation data

collapse-ggtree

Description

collapse a selected clade, which can later be expanded with the 'expand()' fuction if necessary

Usage

## S3 method for class 'ggtree'
collapse(x = NULL, node, mode = "none", clade_name = NULL, ...)

Arguments

x	tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.
node	internal node number
mode	one of 'none'(default), 'max', 'min' and 'mixed'. 'none' would simply collapse the clade as 'tip' and the rest will display a triangle, whose shape is determined by the farest/closest tip of the collapsed clade to indicate it
clade_name	set a name for the collapsed clade. If clade_name = NULL, do nothing
...	additional parameters to set the color or transparency of the triangle

Value

tree view

Author(s)

Guangchuang Yu

See Also

expand

Examples

x <- rtree(15)
p <- ggtree(x) + geom_tiplab()
p
p1 <- collapse(p, node = 17, mode = "mixed", 
               clade_name = "cclade", alpha = 0.8, 
               color = "grey", fill = "light blue")

YuLab-SMU/ggtree documentation built on April 15, 2024, 5:19 p.m.