In xiangpin/ggadd: An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

ggtreeExtra: An R Package To Add Geom Layers On Circular Or Other Layout Tree Of "ggtree".

library(badger)

r badge_bioc_release("ggtreeExtra", "green") r badge_devel("YuLab-SMU/ggtreeExtra", "green")

cat(packageDescription('ggtreeExtra')$Description)

:writing_hand: Author

Shuangbin Xu and GuangChuang Yu

School of Basic Medical Sciences, Southern Medical University.

If you use ggtreeExtra in published research. Please cite the paper:

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang^*^, X Bo^*^ and G Yu^*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166.

• Source code to produce Supplementary Material

:arrow_double_down: Installation

The development version from github:

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("xiangpin/ggtreeExtra")

The released version from Bioconductor:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("ggtreeExtra")

:beginner: Usage

Please refer to the online vignette.

library(ggtreeExtra)
library(ggtree)
library(ggplot2)
library(treeio)
library(ggnewscale)
library(ggstar)

trfile <- system.file("extdata", "tree.nwk", package="ggtreeExtra")
tippoint1 <- system.file("extdata", "tree_tippoint_bar.csv", package="ggtreeExtra")
ring1 <- system.file("extdata", "first_ring_discrete.csv", package="ggtreeExtra")
ring2 <- system.file("extdata", "second_ring_continuous.csv", package="ggtreeExtra")
ringpoint <- system.file("extdata", "second_ring_point.csv", package="ggtreeExtra")

tr <- read.tree(trfile)
dat1 <- read.csv(tippoint1)
dat2 <- read.csv(ring1)
dat3 <- read.csv(ring2)

p <- ggtree(tr, layout="fan", size=0.1, open.angle=10) + 
    geom_treescale(x=6, y=0, linesize=0.2, fontsize=1.2)

p1 <- p %<+% dat1 + 
          geom_star(mapping=aes(fill=Location, size=Length, starshape=Group),
                    starstroke=0.2) +
          scale_size_continuous(range=c(1, 3),
                                guide=guide_legend(keywidth=0.5, keyheight=0.5, override.aes=list(starshape=15), order=2)) +
          scale_fill_manual(values=c("#D15FEE","#EE6A50","#FFC0CB","#8E8E38","#9ACD32","#006400","#8B4513"),
                            guide="none")+
          scale_starshape_manual(values=c(1, 15),
                                 guide=guide_legend(keywidth=0.5, keyheight=0.5, order=1),
                                 na.translate=FALSE)

p2 <- p1 +new_scale_fill()+ 
          geom_fruit(data=dat2,
                      geom=geom_tile,
                      mapping=aes(y=ID, x=Pos, fill=Type),
                      offset=0.08,
                      pwidth=0.25) +
          scale_fill_manual(values=c("#339933", "#dfac03"),
                            guide=guide_legend(keywidth=0.5, keyheight=0.5, order=3)) +
          geom_axis_text(angle=-45, hjust=0)

p3 <- p2 + new_scale_fill()+
           geom_fruit(data=dat3,
                       geom=geom_tile,
                       mapping=aes(y=ID, x=Type2, alpha=Alpha, fill=Type2),
                       pwidth=0.15)+
          scale_fill_manual(values=c("#b22222", "#005500", "#0000be", "#9f1f9f"),
                            guide=guide_legend(keywidth=0.5, keyheight=0.5, order=4)) +
          scale_alpha_continuous(range=c(0, 0.4),
                                guide=guide_legend(keywidth=0.5, keyheight=0.5, order=5)) +
          geom_axis_text(angle=-45, hjust=0)

p4 <- p3 + new_scale_fill()+
           geom_fruit(data=dat1,
                       geom=geom_bar,
                       mapping=aes(y=ID, x=Abundance, fill=Location),
                       pwidth=0.4,
                       stat="identity",
                       orientation="y")+
           geom_axis_text(angle=-45, hjust=0) +
           scale_fill_manual(values=c("#D15FEE","#EE6A50","#FFC0CB","#8E8E38","#9ACD32","#006400","#8B4513"),
                             guide=guide_legend(keywidth=0.5, keyheight=0.5, order=6)) +
           theme(legend.position=c(0.96, 0.5),
                 legend.background=element_rect(fill=NA),
                 legend.title=element_text(size=7),
                 legend.text=element_text(size=6),
                 legend.spacing.y = unit(0.02, "cm"))
p4

:sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

xiangpin/ggadd documentation built on Nov. 6, 2024, 11:04 p.m.