facet-plot: facet_plot

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

Description

plot tree associated data in an additional panel

Usage

facet_plot(p, mapping = NULL, data, geom, panel, ...)

geom_facet(mapping = NULL, data, geom, panel, ...)

Arguments

p	tree view
mapping	aes mapping for 'geom'
data	data to plot by 'geom', first column should be matched with tip label of tree
geom	geom function to plot the data
panel	panel name for plot of input data
...	additional parameters for 'geom'

Details

'facet_plot()' automatically re-arranges the input 'data' according to the tree structure, visualizes the 'data' on specific 'panel' using the 'geom' function with aesthetic 'mapping' and other parameters, and align the graph with the tree 'p' side by side. 'geom_facet' is a 'ggplot2' layer version of 'facet_plot'

Value

ggplot object

Author(s)

Guangchuang Yu

References

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

Examples

tr <- rtree(10)
dd = data.frame(id=tr$tip.label, value=abs(rnorm(10)))
p <- ggtree(tr)
facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))

Example output

Loading required package: ggplot2
Loading required package: treeio
ggtree v1.8.2  For help: https://guangchuangyu.github.io/ggtree

If you use ggtree in published research, please cite:
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.