geom-hilight: geom_hilight

Description Usage Arguments Details Value Aesthetics Author(s) Examples

Description

layer of hilight clade

Usage

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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):

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

Author(s)

Guangchuang Yu and Shuangbin Xu

Examples

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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.