我用 Vphylomaker 制作了系统发育树状图,并用 ggtree 绘制。
这是一个数据示例。
species <- c("Physaliastrum japonicum", "Azolla imbricata", "Ligularia sibirica","Silene repens var. apoiensis", "Eriocaulon amanoanum")
genus <- c("Physaliastrum", "Azolla", "Ligularia", "Silene", "Eriocaulon")
family <- c("Solanaceae","Salviniaceae","Asteraceae","Caryophyllaceae","Eriocaulaceae")
traits <- c("Forest","Wetland","Lake","Forest","Lake")
data <-data.frame(cbind(species,genus,family,traits))
devtools::install_github("jinyizju/V.PhyloMaker")
library("V.PhyloMaker") # load the package
example <- data.frame(data[,1:3]) # input example species list
tree.a <- phylo.maker(sp.list = example, tree = GBOTB.extended, nodes = nodes.info.1, scenarios="S1") # generate the phylogeny
library("ape")
library("Biostrings")
library("ggplot2")
library("ggtree")
ggtree(tree.a$scenario.1,layout="fan", open.angle=0)+
geom_tiplab()
我想根据“数据”中的特征(森林、湿地等)信息为标签(物种)着色。