R包ggtreeExtra绘制进化树

if(!requireNamespace("remotes", quietly=TRUE)){ install.packages("remotes") } remotes::install_github("YuLab-SMU/ggtreeExtra") if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ggtreeExtra") BiocManager::install("ggstar") # 下载"ggstar","ggplot2","ggtree","treeio","ggnewscale"包 install.packages("ggstar") install.packages("ggplot2") install.packages("ggtree") install.packages("treeio") install.packages("ggnewscale") 

library(ggtreeExtra) # 设置叠加的包 library(ggstar) # 提供几何图形 library(ggplot2) # library(ggtree) # 绘制进化树 library(treeio) library(ggnewscale) # 创建新的scale，多个fill或者color 

setwd("D:/R/ggtreeExtra") 

# 树状图数据来源路径 trfile <- system.file("extdata", "tree.nwk", package="ggtreeExtra") # 绘制点图和柱状图的数据来源路径 tippoint1 <- system.file("extdata", "tree_tippoint_bar.csv", package="ggtreeExtra") # 树外第一层的绘制热图来数据源路径 ring1 <- system.file("extdata", "first_ring_discrete.csv", package="ggtreeExtra") # 树外第二层的绘制热图来数据源路径 ring2 <- system.file("extdata", "second_ring_continuous.csv", package="ggtreeExtra") 

tree <- read.tree(trfile) data = fortify(tree) head(data) 

# 可视化进化树，这里图形选用的是"fan"，还可以是 'rectangular', 'dendrogram', 'slanted', 'ellipse', 'roundrect', 'circular', 'circular', 'inward_circular', 'radial', 'equal_angle', 'daylight' or 'ape' p <- ggtree(tree, layout="fan", open.angle=10, size=0.5) p 

dat1 <- read.csv(tippoint1) knitr::kable(head(dat1)) dat2 <- read.csv(ring1) knitr::kable(head(dat2)) dat3 <-read.csv(ring2) knitr::kable(head(dat3)) head(dat3) 

p2 <- p + geom_fruit( data=dat1, geom=geom_star, mapping=aes(y=ID, fill=Location, size=Length, starshape=Group), position="identity", starstroke=0.2 ) + scale_size_continuous( range=c(1, 3), # 大小范围 guide=guide_legend( keywidth=0.5,  # 箱体宽度0.5 Keyheight=0.5, # 箱体宽度0.5 override.aes=list(starshape=15), order=2 ) ) + scale_fill_manual( values=c("#F8766D", "#C49A00", "#53B400", "#00C094", "#00B6EB", "#A58AFF", "#FB61D7"), guide="none" ) + scale_starshape_manual( values=c(1, 15), guide=guide_legend( keywidth=0.5, keyheight=0.5, order=1 ) ) p2 

p3 <- p2 + new_scale_fill() + geom_fruit( data=dat2, geom=geom_tile, mapping=aes(y=ID, x=Pos, fill=Type), offset=0.08,   # 外部层之间的距离，默认为树的 x 范围的0.03倍。 pwidth=0.25  # 外部层的宽度，默认为树的 x 范围的0.2倍。 ) + scale_fill_manual( values=c("#339933", "#dfac03"), guide=guide_legend( keywidth=0.5, keyheight=0.5, order=3 ) ) p3 

p4 <- p3 + new_scale_fill() + geom_fruit( data=dat3, geom=geom_tile, mapping=aes(y=ID, x=Type2, alpha=Alpha, fill=Type2), pwidth=0.15, axis.params=list( axis="x", # 添加图层的轴文本 text.angle=-45, #x 轴的文本角度 hjust=0  # 调整文字轴的水平位置 ) ) + 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), # alpha的范围 guide=guide_legend(keywidth=0.5, keyheight=0.5, order=5) ) p4 

p5 <- p4 + new_scale_fill() + geom_fruit( data=dat1, geom=geom_bar, mapping=aes(y=ID, x=Abundance, fill=Location),  # dat 1的Abundance将被映射到 x pwidth=0.4, stat="identity", orientation="y", # 轴的方向 axis.params=list( axis="x", # 添加图层的轴文本 text.angle=-45, # 轴的文字大小 hjust=0  # 调整轴文本的水平位置 ), grid.params=list() # 添加外部条形图的网格线 ) + scale_fill_manual( values=c("#F8766D", "#C49A00", "#53B400", "#00C094", "#00B6EB", "#A58AFF", "#FB61D7"), guide=guide_legend(keywidth=0.5, keyheight=0.5, order=6) ) + theme(#legend.position=c(0.96, 0.5), # 图例位置 legend.background=element_rect(fill=NA), # 图例背景 legend.title=element_text(size=7), # 图例标题大小 legend.text=element_text(size=6), # 图例文本标签大小 legend.spacing.y = unit(0.02, "cm")  # 调节y轴图例的距离 ) p5