geom-hilight: geom_hilight

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

Description

layer of hilight clade

Usage

geom_hilight(data = NULL, mapping = NULL, node = NULL, type = "auto", ...)

geom_highlight(data = NULL, mapping = NULL, node = NULL, type = "auto", ...)

Arguments

data	data.frame, The data to be displayed in this layer, default is NULL.
mapping	Set of aesthetic mappings, default is NULL.
node	selected node to hilight, when data and mapping is NULL, it is required.
type	the type of layer, default is auto, meaning rectangular, circular, slanted, fan, inward_circular, radial, equal_angle, ape layout tree will use rectangular layer, unrooted and daylight layout tree use will use encircle layer. You can specify this parameter to rect (rectangular layer) or encircle (encircle layer).
...	additional parameters, see also Aesthetics section.

Details

geom_hilight supports data.frame as input. And aesthetics of layer can be mapped. you can see the Aesthetics section to set parameters.

Value

a list object.

Aesthetics

geom_hilight() understands the following aesthetics for rectangular layer (required aesthetics are in bold):

• node selected node to hight light, it is required.

• colour the colour of margin, default is NA.

• fill the colour of fill, default is 'steelblue'.

• alpha the transparency of fill, default is 0.5.

• extend extend xmax of the rectangle, default is 0.

• extendto specify a value, meaning the rectangle extend to, default is NULL.

• linetype the line type of margin, default is 1.

• size the width of line of margin, default is 0.5.

geom_hilight() understands the following aesthethics for encircle layer (required aesthetics are in bold):

• node selected node to hight light, it is required.

• colour the colour of margin, default is 'black'.

• fill the colour of fill, default is 'steelblue'.

• alpha the transparency of fill, default is 0.5.

• expand expands the xspline clade region, default is 0.

• spread control the size, when only one point.

• size the width of line of margin, default is 0.5.

• linetype the line type of margin, default is 1.

• s_shape the shape of the spline relative to the control points, default is 0.5.

• s_open whether the spline is a line or a closed shape, default is FALSE.

Author(s)

Guangchuang Yu and Shuangbin Xu

Examples

library(ggplot2)
set.seed(102)
tree <- rtree(60)
p <- ggtree(tree)
p1 <- p + geom_hilight(node=62) + geom_hilight(node=88, fill="red")
p1
dat <- data.frame(id=c(62, 88), type=c("A", "B"))
p2 <- p + geom_hilight(data=dat, mapping=aes(node=id, fill=type))
p2

Example output

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
ggtree v2.4.1  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
[36m-[39m 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
[36m-[39m 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

ggtree documentation built on Nov. 15, 2020, 2:09 a.m.