R/qDplot.R

In xinghuq/HierD: R package for calculating hierarchical diversity across metrixs and scales, from genes to ecosystem

## The function to plot diversity (q=1,2,3)

qDplot=function(x,q,ncode){ # q=1,2,3
  D00=qD(x,q=0,ncode)
  D11=qD(x,q=1,ncode)
  D22=qD(x,q=2,ncode)
  D0=colMeans(D00)
  D1=colMeans(D11)
  D2=colMeans(D22)

  require(ggplot2)
  if (q==0) {
    data=melt(D0)
    data=data.frame(popname=rownames(data),D0)
    p=ggplot(data,aes(x=popname,y=D0,group =1)) +geom_line(size=1)+ylim(0,(max(D0)+5))+ylab(paste("Diversity q=",q))+xlab("Populations")+geom_point(size=1)+theme(axis.text.x = element_text(angle = 30, hjust = 1))
  }
  else if (q==1) {
    data=melt(D1)
    data=data.frame(popname=rownames(data),D1)
    p=ggplot(data,aes(x=popname,y=D1,group =1)) +geom_line(size=1)+ylim(0,(max(D1)+5))+ylab(paste("Diversity q=",q))+xlab("Populations")+geom_point(size=1)+theme(axis.text.x = element_text(angle = 30, hjust = 1))
  }
  else if (q==2) {
    data=melt(D2)
    data=data.frame(popname=rownames(data),D2)
    p=ggplot(data,aes(x=popname,y=D2,group =1)) +geom_line(size=1)+ylim(0,(max(D2)+5))+ylab(paste("Diversity q=",q))+xlab("Populations")+geom_point(size=1)+theme(axis.text.x = element_text(angle = 30, hjust = 1))
  }
  else if (q=="all") {
    qtotal=cbind(D0,D1,D2)
    rownames(qtotal)=gsub(",","",rownames(qtotal))
    require(reshape2)
    data=melt(qtotal)
    colnames(data)=c("Populations","qD","Diversity")
   p=ggplot(data, aes(x=Populations, y=Diversity, group = qD, colour = qD)) +ylab("Diversity")+xlab("Populations")+geom_line(size=1)+ylim(0,(max(data$Diversity)+5))+geom_point(aes(shape=qD),size=2)+theme(axis.text.x = element_text(angle = 30, hjust = 1))
  }
  else {stop("none of the q is workable")}
return(p)
}