geom_point2: geom_point2

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

geom_point2

Description

geom_point2 is a modified version of geom_point that supports aes(subset)

Usage

geom_point2(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  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().
stat	Name of the statistical transformation to be used on the data for this layer.
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_point2 creates scatterplots, just similar to ggplot2::geom_point. It extends the ggplot2::geom_point to support filtering via the subset aesthetic mapping (see Aesthetics section).

Value

point layer

Aesthetics

geom_point2() understands the following aesthetics

• subset logical expression indicating elements or rows to keep: missing values are taken as false; should be in aes().

• colour the colour of point, defaults to "black".

• fill the colour of fill, defaults to "black".

• alpha the transparency of fill, defaults to 1.

• size the size of point, defaults to 1.5.

• shape specify a shape, defaults to 19.

• stroke control point border thickness of point, defaults to 0.5.

Author(s)

Guangchuang Yu

References

1. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628

2. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. https://doi.org/10.1093/molbev/msy194

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

For more information about tree visualization, please refer to the online book https://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)
## add point by aes(subset)
tr <- rtree(10)
# group tip and node
ggtree(tr) + geom_point2(aes(shape=isTip, color=isTip), size=3)
# specify a node to display
ggtree(tr) + geom_point2(aes(subset=(node==15)), shape=21, size=5, fill='green')
# specify a tip to display
ggtree(tr) + geom_point2(aes(subset=(label %in% c("t1", "t3"))), shape=21, size=5, fill='green')

## color point with continuous variables
library(ggtree)
library(treeio)
library(ggplot2)
beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree")
beast_tree <- read.beast(beast_file)
p <- ggtree(beast_tree) +
  geom_tiplab(hjust = -.1)+ 
  geom_nodepoint(aes(fill = rate), shape = 21, size = 4) +
  scale_fill_continuous(low = 'blue', high = 'red') +
  theme_tree2() + theme(legend.position = 'right')
p

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