S.PhyloMaker是一款用于生物系统学研究的软件工具，主要用于构建和分析种系发生树（也称为进化树）。以下是对S.PhyloMaker的详细介绍：
S.PhyloMaker的使用步骤和一些常用命令的介绍：
安装S.PhyloMaker包：
???????? install.packages("S.PhyloMaker")
加载S.PhyloMaker包：
???????? library(S.PhyloMaker)创建物种分支（phylogenies）：
????????a. 从NCBI进行下载： download.ncbi()
????????b. 使用自定义数据创建： create.phylo(file, format)
读取物种分支：
?????????a. 从NCBI下载的phylo文件： read.ncbi(file)
????????b. 从指定文件中读取phylo文件： read.phylo(file, format)
转换物种分支的格式：
????????a. 转换至ape包的phylo对象格式： to.ape(file)
? ? ? ? b. 转换至phylotools包的phylo4d对象格式： to.phylo4d(file)
物种分支的可视化：
????????a. 绘制物种分支树状图： plot.phylo(file)
????????b. 绘制分支颜色标签（branch color）： plot.phylo(file, color)
物种分支的编辑和处理：
????????a. 删除物种分支： prune.phylo(file, species)
????????b. 裁剪物种分支的范围： crop.phylo(file, start, end)
????????c. 在物种分支上添加标签： label.phylo(file, labels)
????????d. 提取物种分支的信息： extract.phylo(file, column)
物种分支数据的导出：
????????a. 导出为NEXUS格式： export.nexus(file, output)
????????b. 导出为Newick格式： export.newick(file, output)
S.PhyloMaker是一个用于处理系统发育数据的R工具包。它可以从原始数据中创建系统发育树，并进行一系列的数据处理和可视化操作。下面是使用步骤和常用命令的介绍：
步骤：
安装R：首先需要安装R语言环境，可以从R官方网站(https://www.r-project.org/)下载对应系统的安装包进行安装。
安装S.PhyloMaker：打开R控制台，在命令行中输入以下命令来安装S.PhyloMaker包：
install.packages("S.PhyloMaker")
library(S.PhyloMaker)
tree <- phylo_maker(data = mydata, type = "raw")
这里，mydata是原始数据，type参数指定数据类型为"raw"。
tree <- phylo_maker(data = "tree_file.nwk", type = "tree")
这里，tree_file.nwk是已有的系统发育树文件路径，type参数指定数据类型为"tree"。
leaves <- get_leaves(tree)
nodes <- get_nodes(tree)
degree <- get_degree(tree)
height <- get_height(tree)
depth <- get_depth(tree)
phylotools_analysis(tree)
plot_tree(tree)
plot_degree(tree)
plot_height(tree)
library("phytools") # load the "phytools" package.
example<-read.csv("example.splist.csv",header=T) # read in the example species list.
phylo<-read.tree("PhytoPhylo.tre") # read in the megaphylogeny.
nodes<-read.csv("nodes.csv",header=T) # read in the nodes information of the megaphylogeny.
result<-S.PhyloMaker(spList=example, tree=phylo, nodes=nodes) # run the function S.PhyloMaker.
str(result) # the structure of the ouput of S.PhyloMaker.
par(mfrow=c(1,3),mar=c(0,0,1,0)) # show the phylogenies of the three scenarios.
plot(result$Scenario.1,cex=1.1,main="Scenarion One")
plot(result$Scenario.2,cex=1.1,main="Scenarion Two")
plot(result$Scenario.3,cex=1.1,main="Scenarion Three")S.PhyloMaker<-function (tree, spList, nodes, output.spList = T, scenarios = c("S1", "S2", "S3"))
{
options(scipen=999)
tree0 <- tree
spList[sapply(spList, is.factor)] <- lapply(spList[sapply(spList, is.factor)], as.character)
if (any(duplicated(spList$species)))
{
warning("Duplicated species detected and removed.")
print(spList$species[duplicated(spList$species)])
}
spList <- spList[!duplicated(spList$species), ]
spList.original <- spList
spList$species <- gsub(" ", "_", spList$species)
spList$species <- gsub("(^[[:alpha:]])", "\\U\\1", spList$species, perl = TRUE)
spList$genus <- gsub("(^[[:alpha:]])", "\\U\\1", spList$genus, perl = TRUE)
spList$family <- gsub("(^[[:alpha:]])", "\\U\\1", spList$family, perl = TRUE)
rnN <- data.frame(node.label = paste("N", 1:length(tree$node.label), sep = ""), oriN = tree$node.label, stringsAsFactors = FALSE)
nodes[,c("level","family","genus","rn","bn","taxa")]<-lapply(nodes[,c("level","family","genus","rn","bn","taxa")], as.character)
tree$node.label <- paste("N", 1:length(tree$node.label), sep = "")
kk<-c()
for (i in 1:length(tree$tip.label)) {
kk<-c(kk,substring(tree$tip.label[i],1,gregexpr("_",tree$tip.label[i])[[1]][1]-1))
}
m<-data.frame(num=1:length(kk),genus=kk,species=tree$tip.label)
m<-merge(m,nodes[,c("genus","family")])
mX <- m
m <- m[,c("genus","family")]
m <- m[!duplicated(m$genus),]
dimnames(m)[[2]][2] <- "family_in_PhytoPhylo"
m<-m[,c("genus","family_in_PhytoPhylo")]
m0 <- spList[!duplicated(spList$genus), c("genus","family")]
dimnames(m0)[[2]][2] <- "family_in_spList"
mm<-merge(m0, m)
g<-mm[which(is.na(match(paste(mm$genus,mm$family_in_spList,sep="_"),paste(mm$genus,mm$family_in_PhytoPhylo,sep="_")))),]
if (dim(g)[1]>0)
{
print("Taxonomic classification not consistent between spList and PhytoPhylo.")
print(g)
}
add.tip <- spList[which(is.na(match(spList$species, tree$tip.label))), ]
status <- rep("match(prune)", dim(spList)[1])
status[which(is.na(match(spList$species, tree$tip.label)))] <- "match(add)"
if (dim(add.tip)[1] == 0 & length(na.omit(match(spList$species, tree$tip.label))) == 0)
stop("Incorrect format of species list.")
if (length(setdiff(spList$species, tree0$tip.label)) == 0 & length(na.omit(match(spList$species, tree$tip.label))) > 0)
{
print("There is no species needs to be added, all the species are pruned from PhytoPhylo.")
splis <- spList.original
treeX <- drop.tip(tree0, setdiff(tree0$tip.label, splis$species))
splis$status <- "match(prune)"
phylo0 <- list(Scenario.1 = NULL, Scenario.2 = NULL, Scenario.3 = NULL, Species.list = splis)
if ("S1" %in% scenarios) {phylo0$Scenario.1 <- treeX}
if ("S2" %in% scenarios) {phylo0$Scenario.2 <- treeX}
if ("S3" %in% scenarios) {phylo0$Scenario.3 <- treeX}
phylo0[sapply(phylo0, is.null)] <- NULL
return(phylo0)
stop()
}
add.tip$sort <- ""
add.tip$sort[which(!is.na(match(add.tip$genus, nodes[nodes$level == "G", ]$genus)))] <- "G1"
add.tip$sort[which(is.na(match(add.tip$genus, nodes[nodes$level == "G", ]$genus)) & !is.na(match(add.tip$family, nodes[nodes$level == "F", ]$family)))] <- "F1"
add.tip$sort[add.tip$sort == "F1"][duplicated(add.tip[add.tip$sort == "F1", ]$genus)] <- "F2"
a <- which(add.tip$sort == "")
if (length(a) > 0)
{
print(paste("Note:", length(a), "taxa unmatch:",sep=" "))
print(add.tip$species[a])
status[match(add.tip$species[a], spList$species)] <- "unmatch"
}
spList.original$status <- status
if ("S1" %in% scenarios) {
t1 <- tree
rnN1<-rnN
nG <- nodes[nodes$level == "G", ]
nF <- nodes[nodes$level == "F", ]
data <- add.tip[add.tip$sort == "F1", ]
if (dim(data)[1] > 0) {
for (i in 1:dim(data)[1]) {
n <- match(data$family[i], nF$family)
g <- nF$gen.n[n]
s <- nF$sp.n[n]
if (g == 1 & s == 1) {
num <- grep(nF$taxa[n], t1$tip.label)
len <- t1$edge.length[match(num, t1$edge[, 2])]
t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num, position = len)
nF$gen.n[n] <- g + 1
nF$sp.n[n] <- s + 1
num <- grep(nF$taxa[n], t1$tip.label)
t1$node.label[match(t1$edge[match(num, t1$edge[, 2]), 1], unique(t1$edge[, 1]))] <- paste("NN", t1$Nnode + 1, sep = "")
rnN1$node.label[match(nF$bn[n], rnN1$node.label)]<- paste("NN", t1$Nnode + 1, sep = "")
nF$bn[n] <- paste("NN", t1$Nnode + 1, sep = "")
nF$bn.bl[n] <- len
}
else {
num <- unique(t1$edge[, 1])[match(nF$bn[n], t1$node.label)]
len <- nF$bn.bl[n]
t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num)
}
}
}
data <- add.tip[add.tip$sort != "F1", ]
if (dim(data)[1] > 0) {
for (i in 1:dim(data)[1]) {
n <- grep(paste(data$genus[i], "_", sep = ""), t1$tip.label)
if (length(n) == 1) {
num <- n
len <- t1$edge.length[match(num, t1$edge[, 2])]
t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num, position = len)
}
if (length(n) > 1) {
num <- fastMRCA(t1, t1$tip.label[min(n)], t1$tip.label[max(n)])
len <- fastDist(t1, t1$tip.label[min(n)], t1$tip.label[max(n)])/2
t1 <- bind.tip(t1, tip.label = data$species[i], edge.length = len, where = num)
}
}
}
toDrop <- setdiff(1:length(t1$tip.label), which(!is.na(match(t1$tip.label, spList$species))))
t1 <- drop.tip(t1, tip = toDrop)
Re <- which(!is.na(match(t1$node.label, rnN1$node.label)))
noRe <- which(is.na(match(t1$node.label, rnN1$node.label)))
t1$node.label[Re] <- rnN1$oriN[match(t1$node.label, rnN1$node.label)[Re]]
t1$node.label[noRe] <- ""
}
else {
t1 <- NULL
}
if ("S2" %in% scenarios) {
t2 <- tree
rnN2<-rnN
nG <- nodes[nodes$level == "G", ]
nF <- nodes[nodes$level == "F", ]
data <- add.tip[add.tip$sort == "F1", ]
if (dim(data)[1] > 0) {
for (i in 1:dim(data)[1]) {
n <- match(data$family[i], nF$family)
g <- nF$gen.n[n]
s <- nF$sp.n[n]
if (g == 1 & s == 1) {
num <- grep(nF$taxa[n], t2$tip.label)
len <- t2$edge.length[match(num, t2$edge[,2])] * sample((1:99)/100,1)
t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
nF$gen.n[n] <- g + 1
nF$sp.n[n] <- s + 1
num <- grep(data$species[i], t2$tip.label)
t2$node.label[match(t2$edge[match(num, t2$edge[, 2]), 1], unique(t2$edge[,1]))] <- paste("NN", t2$Nnode + 1, sep = "")
rnN2$node.label[match(nF$bn[n], rnN2$node.label)]<- paste("NN", t2$Nnode + 1, sep = "")
nF$bn[n] <- paste("NN", t2$Nnode + 1, sep = "")
nF$bn.bl[n] <- len
}
else {
num <- unique(t2$edge[, 1])[match(nF$bn[n], t2$node.label)]
len <- t2$edge.length[match(num,t2$edge[,2])] * sample((1:99)/100,1)
t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
nF$gen.n[n] <- g + 1
nF$sp.n[n] <- s + 1
num <- grep(data$species[i], t2$tip.label)
t2$node.label[match(t2$edge[match(num, t2$edge[, 2]), 1], unique(t2$edge[, 1]))] <- paste("NN", t2$Nnode + 1, sep = "")
rnN2$node.label[match(nF$bn[n], rnN2$node.label)]<- paste("NN", t2$Nnode + 1, sep = "")
nF$bn[n] <- paste("NN", t2$Nnode + 1, sep = "")
nF$bn.bl[n] <- nF$bn.bl[n]+len
}
}
}
data <- add.tip[add.tip$sort != "F1", ]
if (dim(data)[1] > 0) {
for (i in 1:dim(data)[1]) {
n <- grep(paste(data$genus[i], "_", sep = ""), t2$tip.label)
if (length(n) == 1) {
num <- n
len <- t2$edge.length[match(num, t2$edge[, 2])] * sample((1:99)/100,1)
t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
}
if (length(n) > 1) {
num <- sample(n,1)
len <- t2$edge.length[match(num, t2$edge[, 2])] * sample((1:99)/100,1)
t2 <- bind.tip(t2, tip.label = data$species[i], edge.length = len, where = num, position = len)
}
}
}
toDrop <- setdiff(1:length(t2$tip.label), which(!is.na(match(t2$tip.label, spList$species))))
t2 <- drop.tip(t2, tip = toDrop)
Re <- which(!is.na(match(t2$node.label, rnN2$node.label)))
noRe <- which(is.na(match(t2$node.label, rnN2$node.label)))
t2$node.label[Re] <- rnN2$oriN[match(t2$node.label, rnN2$node.label)[Re]]
t2$node.label[noRe] <- ""
}
else {
t2 <- NULL
}
if ("S3" %in% scenarios) {
t3 <- tree
rnN3<-rnN
nG <- nodes[nodes$level == "G", ]
nF <- nodes[nodes$level == "F", ]
data <- add.tip[add.tip$sort == "F1", ]
if (dim(data)[1] > 0) {
for (i in 1:dim(data)[1]) {
n <- match(data$family[i], nF$family)
g <- nF$gen.n[n]
s <- nF$sp.n[n]
if (g == 1 & s == 1) {
num <- grep(nF$taxa[n], t3$tip.label)
len <- t3$edge.length[match(num, t3$edge[, 2])] * (2/3)
t3 <- bind.tip(t3, tip.label = data$species[i], edge.length = len, where = num, position = len)
nF$gen.n[n] <- g + 1
nF$sp.n[n] <- s + 1
num <- grep(nF$taxa[n], t3$tip.label)
t3$node.label[match(t3$edge[match(num, t3$edge[, 2]), 1], unique(t3$edge[, 1]))] <- paste("NN", t3$Nnode + 1, sep = "")
rnN3$node.label[match(nF$bn[n], rnN3$node.label)]<- paste("NN", t3$Nnode + 1, sep = "")
nF$bn[n] <- paste("NN", t3$Nnode + 1, sep = "")
nF$bn.bl[n] <- len
}
if (g == 1 & s > 1) {
num <- unique(t3$edge[, 1])[match(nF$bn[n], t3$node.label)]
if ((2/3)*nF$rn.bl[n] <= nF$bn.bl[n]) { len <-(nF$rn.bl[n]-nF$bn.bl[n])/2 }
if ((2/3)*nF$rn.bl[n] > nF$bn.bl[n]) { len <-nF$rn.bl[n]*2/3-nF$bn.bl[n] }
t3 <- bind.tip(t3, tip.label = data$species[i], edge.length = len, where = num, position = len)
nF$gen.n[n] <- g + 1
nF$sp.n[n] <- s + 1
num <- unique(t3$edge[, 1])[match(nF$bn[n], t3$node.label)]
t3$node.label[match(t3$edge[match(num, t3$edge[, 2]), 1], unique(t3$edge[, 1]))] <- paste("NN", t3$Nnode + 1, sep = "")
rnN3$node.label[match(nF$bn[n], rnN3$node.label)]<- paste("NN", t3$Nnode + 1, sep = "")
nF$bn[n] <- paste("NN", t3$Nnode + 1, sep = "")
nF$bn.bl[n] <- len+nF$bn.bl[n]
}
if (g > 1) {
num <- unique(t3$edge[, 1])[match(nF$bn[n], t3$node.label)]
len <- nF$bn.bl[n]
t3 <- bind.tip(t3, tip.label = data$species[i], edge.length = len, where = num)
}
}
}
data <- add.tip[add.tip$sort != "F1", ]
if (dim(data)[1] > 0) {
for (i in 1:dim(data)[1]) {
n <- grep(paste(data$genus[i], "_", sep = ""), t3$tip.label)
if (length(n) == 1) {
len <- t3$edge.length[match(n, t3$edge[, 2])]/2
t3 <- bind.tip(t3, tip.label = data$species[i], edge.length = len, where = n, position = len)
nG$sp.n[match(data$genus[i], nG$genus)] <- length(n) + 1
nu <- grep(paste(data$genus[i], "_", sep = ""), t3$tip.label)
num <- fastMRCA(t3, t3$tip.label[nu[1]], t3$tip.label[nu[2]])
t3$node.label[match(num, unique(t3$edge[, 1]))] <- paste("NN", t3$Nnode + 1, sep = "")
rnN3$node.label[match(nG$bn[n], rnN3$node.label)]<- paste("NN", t3$Nnode + 1, sep = "")
nG$bn[match(data$genus[i], nG$genus)] <- paste("NN", t3$Nnode + 1, sep = "")
nG$bn.bl[match(data$genus[i], nG$genus)] <- len
}
if (length(n) > 1) {
num <- fastMRCA(t3, t3$tip.label[min(n)], t3$tip.label[max(n)])
len <- as.numeric(branching.times(t3))[match(num, unique(t3$edge[, 1]))]
t3 <- bind.tip(t3, tip.label = data$species[i], edge.length = len, where = num)
}
}
}
toDrop <- setdiff(1:length(t3$tip.label), which(!is.na(match(t3$tip.label, spList$species))))
t3 <- drop.tip(t3, tip = toDrop)
Re <- which(!is.na(match(t3$node.label, rnN3$node.label)))
noRe <- which(is.na(match(t3$node.label, rnN3$node.label)))
t3$node.label[Re] <- rnN3$oriN[match(t3$node.label, rnN3$node.label)[Re]]
t3$node.label[noRe] <- ""
}
else {
t3 <- NULL
}
if (output.spList == FALSE)
spList <- NULL
phylo <- list(Scenario.1 = t1, Scenario.2 = t2, Scenario.3 = t3, Species.list = spList.original)
phylo[sapply(phylo, is.null)] <- NULL
return(phylo)
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