R/match.name.r

In iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

match.name<-function(name.check=integer(0),rn.list=list(integer(0)),cn.list=list(integer(0)),both.list=list(integer(0)),
                     v.list=list(integer(0)),lf.list=list(integer(0)),tree.list=list(integer(0)),group=integer(0),rerank=TRUE,silent=FALSE)
{
  if(length(name.check)==0)
  {
    if(length(tree.list[[1]])!=0){tname1=tree.list[[1]]$tip.label}else{tname1=integer(0)}
    name.check=unique(c(rownames(rn.list[[1]]),colnames(cn.list[[1]]),colnames(both.list[[1]]),names(v.list[[1]]),names(lf.list[[1]]),tname1))
  }
  
  namelist<-function(aa,prefix=integer(0))
  {
    if(length(names(aa))==0)
    {
      names(aa)=paste(prefix,1:length(aa),sep=".")
    }else{
      for(i in 1:length(aa))
      {
        if(nchar(names(aa)[i])==0){names(aa)[i]=paste(prefix,i,sep=".")}
      }
    }
    aa
  }
  
  if(length(rn.list[[1]])!=0)
  {
    rn.list=namelist(rn.list,prefix="rn.list")
    rname.list=lapply(1:length(rn.list), function(i,rl){rownames(rl[[i]])},rl=rn.list)
    names(rname.list)=paste(names(rn.list),".rowname",sep = "")
  }else{
    rname.list<-rn.list<-integer(0)
  }
  
  if(length(cn.list[[1]])!=0)
  {
    cn.list=namelist(cn.list,prefix="cn.list")
    cname.list=lapply(1:length(cn.list), function(i,rl){colnames(rl[[i]])},rl=cn.list)
    names(cname.list)=paste(names(cn.list),".colname",sep = "")
  }else{
    cname.list<-cn.list<-integer(0)
  }

  if(length(both.list[[1]])!=0)
  {
    both.list=namelist(both.list,prefix="both.list")
    bname.r.list=lapply(1:length(both.list), function(i,rl){rownames(rl[[i]])},rl=both.list)
    names(bname.r.list)=paste(names(both.list),".rowname",sep = "")
    bname.c.list=lapply(1:length(both.list), function(i,rl){colnames(rl[[i]])},rl=both.list)
    names(bname.c.list)=paste(names(both.list),".colname",sep = "")
    bname.list=c(bname.r.list,bname.c.list)
  }else{
    bname.list<-both.list<-integer(0)
  }
  
  if(length(v.list[[1]])!=0)
  {
    v.list=namelist(v.list,prefix="v.list")
    vname.list=lapply(1:length(v.list),function(i,rl){names(rl[[i]])},rl=v.list)
    names(vname.list)=paste0(names(v.list),".vname")
  }else{
    vname.list<-v.list<-integer(0)
  }
  
  if(length(lf.list[[1]])!=0)
  {
    lf.list=namelist(lf.list,prefix="lf.list")
    fname.list=lapply(1:length(lf.list),function(i,rl){names(rl[[i]])},rl=lf.list)
    names(fname.list)=paste0(names(lf.list),".name")
  }else{
    fname.list<-lf.list<-integer(0)
  }
  
  if(length(tree.list[[1]])!=0)
  {
    tree.list=namelist(tree.list,prefix = "tree.list")
    tname.list=lapply(1:length(tree.list),function(i,rl){rl[[i]]$tip.label},rl=tree.list)
    names(tname.list)=paste0(names(tree.list),".tipname")
  }else{
    tname.list<-tree.list<-integer(0)
  }
  
  if(length(group)!=0)
  {
    if(is.data.frame(group)|is.matrix(group))
    {
      if(ncol(group)>1){warning("Group has more than one column, only the first column was used. ",date())}
      group=as.matrix(group)[,1,drop=FALSE]
      if(is.null(rownames(group)))
      {
        if(nrow(group)!=length(name.check)){stop("Group does not have the same length as expected. ",date())}else{
          warning("Group has no names. The checked name list was assigned to Group.")
          rownames(group)=name.check
        }
      }
      gname.list=list(group.name=rownames(group))
    }else if(is.vector(group)|is.factor(group)){
      if(is.null(names(group)))
      {
        if(length(group)!=length(name.check)){stop("Group does not have the same length as expected. ",date())}else{
          warning("Group has no names. The checked name list was assigned to Group.")
          group=matrix(group,ncol=1)
          rownames(group)=name.check
        }
      }else{
        gname.list=list(group.name=names(group))
        grp=matrix(as.vector(group),ncol=1)
        rownames(grp)=names(group)
        group=grp
      }
    }else{stop("The format of Group can only be vector, factor, data.frame, or matrix. others are not acceptable. ", date)}
  }else{gname.list=integer(0)}
  
  lname.list=c(rname.list,cname.list,bname.list,vname.list,fname.list,tname.list,gname.list)
  lntn.list=c(rname.list,cname.list,bname.list,vname.list,fname.list,gname.list)
  if(length(lntn.list)>0)
  {
    tot.mis=sum(sapply(lntn.list, function(oldname,name.check){if(length(oldname)==length(name.check)){sum(oldname!=name.check)}else{1}},name.check=name.check))
  }else{tot.mis=0}
  if(length(tname.list)>0)
  {
    tot.mis=tot.mis+sum(sapply(tname.list, function(oldname,name.check){sum(!(name.check %in% oldname))+sum(!(oldname %in% name.check))},name.check=name.check))
  }
  
  if(tot.mis==0)
  {
    if(!silent) message("All match very well.")
    output=c(rn.list,cn.list,both.list,v.list,lf.list,tree.list,group)
  }else{
    check.name<-function(i,lname.list,name.check)
    {
      cname=lname.list[[i]]
      los.id=(!(name.check %in% cname))
      add.id=(!(cname %in% name.check))
      mis=sum(add.id)+sum(los.id)
      if(mis>0)
      {
        if(!silent) message("Mismatch warning: ",names(lname.list)[i]," has ",mis," mismatched names. ")
        if(!silent) if(sum(los.id)>0) message("lost name: ", paste(name.check[los.id]," ",sep = ""))
        if(!silent) if(sum(add.id)>0) message("unexpected name: ",paste(cname[add.id]," ",sep = ""))
      }
      mis
    }
    checked=sapply(1:length(lname.list), check.name,lname.list=lname.list,name.check=name.check)
    output=checked
    if(rerank)
    {
      if(sum(checked)>0)
      {
        lname.list=c(list(name.check),lname.list)
        iname=Reduce(intersect,lname.list)
      }else{iname=name.check}
      
      if(is.list(rn.list))
      {
        rn.list.new=lapply(rn.list, function(old,iname){old[match(iname,rownames(old)),,drop=FALSE]},iname=iname)
        names(rn.list.new)=names(rn.list)
      }else{rn.list.new=integer(0)}
      
      if(is.list(cn.list))
      {
        cn.list.new=lapply(cn.list, function(old,iname){old[,match(iname,colnames(old)),drop=FALSE]},iname=iname)
        names(cn.list.new)=names(cn.list)
      }else{cn.list.new=integer(0)}
      
      if(is.list(both.list))
      {
        both.list.new=lapply(both.list, function(old,iname){old[match(iname,rownames(old)),match(iname,colnames(old)),drop=FALSE]},iname=iname)
        names(both.list.new)=names(both.list)
      }else(both.list.new=integer(0))
      
      if(is.list(v.list))
      {
        v.list.new=lapply(v.list,function(old,iname){old[match(iname,names(old))]},iname=iname)
        names(v.list.new)=names(v.list)
      }else{v.list.new=integer(0)}
      
      if(is.list(lf.list))
      {
        f.list.new=lapply(lf.list,function(old,iname){old[match(iname,names(old))]},iname=iname)
        names(f.list.new)=names(lf.list)
      }else{f.list.new=integer(0)}
      
      if(is.list(tree.list))
      {
        requireNamespace("ape")
        tree.list.new=lapply(tree.list,function(tr,iname){rm.tip=tr$tip.label[!(tr$tip.label %in% iname)];ape::drop.tip(tr,rm.tip)},iname=iname)
        names(tree.list.new)=names(tree.list)
      }else{tree.list.new=integer(0)}
      
      if(length(group)!=0)
      {
        group.new=list(group=group[match(iname,rownames(group)),,drop=FALSE])
      }else{group.new=integer(0)}
      
      output=c(rn.list.new,cn.list.new,both.list.new,v.list.new,f.list.new,tree.list.new,group.new)
      if(!silent) message("The names are re-ranked.")
    }
  }
  output
}