geom_rootpoint: geom_rootpoint

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

geom_rootpoint

Description

geom_rootpoint is used to add root point layer to a tree

Usage

geom_rootpoint(
  mapping = NULL,
  data = NULL,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

Arguments

mapping	Set of aesthetic mapping created by aes(). If inherit.aes = TRUE, the mapping can be inherited from the plot mapping as specified in the call to ggplot().
data	The data to be displayed in this layer. If 'NULL' (the default), the data is inherited from the plot data as specified in the call to ggplot().
position	Position adjustment.
na.rm	logical. If 'FALSE' (default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? 'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.
inherit.aes	logical (defaults to 'TRUE'). If 'FALSE', overrides the default aesthetics, rather then combining with them.
...	addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3.

Details

geom_rootpoint inherit from geom_point2, and it is used to display and customize the points on the root

Value

root point layer

Author(s)

Guangchuang Yu

References

1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96

2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194

3. 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. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628

For more information, please refer to the online book:Data Integration, Manipulation and Visualization of Phylogenetic Trees.http://yulab-smu.top/treedata-book/

See Also

geom_point; geom_rootpoint add point of root; geom_nodepoint add points of internal nodes; geom_tippoint add points of external nodes (also known as tips or leaves).

Examples

library(ggtree)
tr <- rtree(10)
##  add root point
ggtree(tr) + geom_rootpoint()
ggtree(tr) + geom_rootpoint(size=2,color="red",shape=2)

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