R/pathview.R

In pathview: a tool set for pathway based data integration and visualization

pathview <-
function(
                         gene.data=NULL,
                         cpd.data=NULL,
#                         xml.file=NULL,
                         pathway.id,
                         species = "hsa",
                         kegg.dir=".",
                   cpd.idtype="kegg",
                   gene.idtype="entrez",
                   gene.annotpkg=NULL,
                   min.nnodes=3,#
         
                   kegg.native=TRUE,
                   map.null=TRUE,
                   expand.node=FALSE, #g
                           split.group=FALSE, #g

                         map.symbol=TRUE,
                         map.cpdname=TRUE, #g
                         
                         node.sum="sum",
         discrete=list(gene=FALSE, cpd=FALSE),
         limit=list(gene=1, cpd=1),
                         bins=list(gene=10, cpd=10),
                         both.dirs=list(gene=T, cpd=T),
                         trans.fun = list(gene = NULL,  cpd = NULL),
         low = list(gene = "green", cpd = "blue"),
                         mid = list(gene = "gray", cpd = "gray"),
                         high = list(gene = "red", cpd = "yellow"),
         na.col="transparent",
         
#                         new.signature=TRUE,
#                         plot.col.key=TRUE,
#                         key.align="x",
#                         key.pos="topright",
#                         sign.pos="bottomright",#g
                         ...){

#length-2 arguments check

  dtypes=!is.null(gene.data)+!is.null(cpd.data)
  cond0=dtypes==1 & is.numeric(limit) & length(limit)>1
  if(cond0){
    if(limit[1]!=limit[2] & is.null(names(limit)))
      limit=list(gene=limit[1:2], cpd=limit[1:2])
  }
  if(is.null(trans.fun)) trans.fun=list(gene = NULL,  cpd = NULL)
  
  arg.len2=c("discrete", "limit","bins", "both.dirs", "trans.fun", "low", "mid", "high")
  for(arg in arg.len2){
    obj1=eval(as.name(arg))
    if(length(obj1)==1) obj1=rep(obj1,2)
    if(length(obj1)>2) obj1=obj1[1:2]
    obj1=as.list(obj1)
    ns=names(obj1)
    if(length(ns)==0 |!all(c("gene", "cpd") %in% ns)) names(obj1)=c("gene", "cpd")
    assign(arg, obj1)
  }

#data.checck
  if(is.character(gene.data)){
    gd.names=gene.data
    gene.data=rep(1, length(gene.data))
    names(gene.data)=gd.names
    both.dirs$gene=FALSE
    ng=length(gene.data)
    nsamp.g=1
  } else if(!is.null(gene.data)){
    if(length(dim(gene.data))==2){
      gd.names=rownames(gene.data)
      ng=nrow(gene.data)
      nsamp.g=2
    } else if(is.numeric(gene.data) & is.null(dim(gene.data))){
      gd.names=names(gene.data)
      ng=length(gene.data)
      nsamp.g=1
    } else stop("wrong gene.data format!")
  } else if(is.null(cpd.data)){
    stop("gene.data and cpd.data are both NULL!")
  }
  gene.idtype=toupper(gene.idtype)
  data(bods)
#  data(gene.idtype.bods)
  if(species!="ko"){
    species.data=kegg.species.code(species, na.rm=T, code.only=FALSE)
  } else {
    species.data=c(kegg.code="ko", entrez.gnodes="0", kegg.geneid="K01488", ncbi.geneid=NA, ncbi.proteinid=NA, uniprot=NA)
    gene.idtype="KEGG"
    msg.fmt="Only KEGG ortholog gene ID is supported, make sure it looks like \"%s\"!"
    msg=sprintf(msg.fmt, species.data["kegg.geneid"])
    message("Note: ", msg)
  }
  if(length(dim(species.data))==2) {
    message("Note: ", "More than two valide species!")
    species.data=species.data[1,]
  }
  species=species.data["kegg.code"]
  entrez.gnodes=species.data["entrez.gnodes"]==1
  if(is.na(species.data["ncbi.geneid"])){
    if(!is.na(species.data["kegg.geneid"])){
      msg.fmt="Mapping via KEGG gene ID (not Entrez) is supported for this species,\nit looks like \"%s\"!"
      msg=sprintf(msg.fmt, species.data["kegg.geneid"])
      message("Note: ", msg)
    } else{
      stop("This species is not annotated in KEGG!")
    }
  }
  if(is.null(gene.annotpkg)) gene.annotpkg=bods[match(species, bods[,3]),1]
  if(length(grep("ENTREZ|KEGG|NCBIPROT|UNIPROT", gene.idtype))<1 & !is.null(gene.data)){
    if(is.na(gene.annotpkg)) stop("No proper gene annotation package available!")
    if(!gene.idtype %in% gene.idtype.bods[[species]]) stop("Wrong input gene ID type!")
    gene.idmap=id2eg(gd.names, category=gene.idtype, pkg.name=gene.annotpkg, unique.map=F)
    gene.data=mol.sum(gene.data, gene.idmap)
    gene.idtype="ENTREZ"
  }

  if(gene.idtype!="KEGG" & !entrez.gnodes & !is.null(gene.data)){
    id.type=gene.idtype
    if(id.type=="ENTREZ") id.type="ENTREZID"
    kid.map=names(species.data)[-c(1:2)]
    kid.types=names(kid.map)=c("KEGG", "ENTREZID", "NCBIPROT", "UNIPROT")
    kid.map2=gsub("[.]", "-", kid.map)
    kid.map2["UNIPROT"]="up"
    if(is.na(kid.map[id.type])) stop("Wrong input gene ID type for the species!")
    message("Info: Getting gene ID data from KEGG...")
    gene.idmap=keggConv(kid.map2[id.type],species)
    message("Info: Done with data retrieval!")
    kegg.ids=gsub(paste(species, ":", sep=""), "", names(gene.idmap))
    in.ids=gsub(paste0(kid.map2[id.type],":"), "", gene.idmap)
    gene.idmap=cbind(in.ids, kegg.ids)
    gene.data=mol.sum(gene.data, gene.idmap)
    gene.idtype="KEGG"
  }

  
  if(is.character(cpd.data)){
    cpdd.names=cpd.data
    cpd.data=rep(1, length(cpd.data))
    names(cpd.data)=cpdd.names
    both.dirs$cpd=FALSE
    ncpd=length(cpd.data)
  } else if(!is.null(cpd.data)){
    if(length(dim(cpd.data))==2){
    cpdd.names=rownames(cpd.data)
    ncpd=nrow(cpd.data)
    } else if(is.numeric(cpd.data) & is.null(dim(cpd.data))){
        cpdd.names=names(cpd.data)
        ncpd=length(cpd.data)
    } else stop("wrong cpd.data format!")
  }
  if(length(grep("kegg", cpd.idtype))<1 & !is.null(cpd.data)){
    data(rn.list)
    cpd.types=c(names(rn.list),"name")
    cpd.types=tolower(cpd.types)
    cpd.types=cpd.types[-grep("kegg", cpd.types)]
    if(!tolower(cpd.idtype) %in% cpd.types) stop("Wrong input cpd ID type!")
    cpd.idmap=cpd2kegg(cpdd.names, in.type=cpd.idtype)
    cpd.data=mol.sum(cpd.data, cpd.idmap)
  }

  
#parse  
  warn.fmt="Parsing %s file failed, please check the file!"

  if(length(grep(species, pathway.id))>0) {
    pathway.name = pathway.id
    pathway.id = gsub(species, "", pathway.id)
  } else pathway.name = paste(species, pathway.id, sep = "")
  kfiles=list.files(path=kegg.dir, pattern="[.]xml|[.]png")
  npath=length(pathway.id)
  out.list=list()#vector(mode = "list", length = npath)
  
  #if(is.null(xml.file) | length(xml.file)!=npath)#custom xml and png file need to have the same names
  tfiles.xml=paste(pathway.name, "xml", sep=".")
  tfiles.png=paste(pathway.name, "png", sep=".")
  if(kegg.native) ttype=c("xml", "png") else ttype="xml"
  xml.file <- paste(kegg.dir, "/", tfiles.xml, sep = "")
  
  for(i in 1:npath){
    ##  out.list=lapply(1:npath, function(i){
    if(kegg.native) tfiles=c(tfiles.xml[i],tfiles.png[i])
    else tfiles=tfiles.xml[i]
    if(!all(tfiles %in% kfiles)){
      dstatus=download.kegg(pathway.id = pathway.id[i], species = species, kegg.dir=kegg.dir, file.type=ttype)
      if(dstatus=="failed") {
        warn.fmt="Failed to download KEGG xml/png files, %s skipped!"
        warn.msg=sprintf(warn.fmt, pathway.name[i])
        message("Warning: ", warn.msg)
        return(invisible(0))#out.list[[i]]=0
      }
    }

  if(kegg.native){
    node.data=try(node.info(xml.file[i]), silent=T)
    if(class(node.data)[1]=="try-error"){
      warn.msg=sprintf(warn.fmt, xml.file[i])
      message("Warning: ", warn.msg)
      return(invisible(0))
    }
    node.type=c("gene","enzyme", "compound", "ortholog")
    sel.idx=node.data$type %in% node.type
    nna.idx=!is.na(node.data$x+node.data$y+node.data$width+node.data$height)
    sel.idx=sel.idx & nna.idx
    if(sum(sel.idx)<min.nnodes){
      warn.fmt="Number of mappable nodes is below %d, %s skipped!"
      warn.msg=sprintf(warn.fmt, min.nnodes, pathway.name[i])
      message("Warning: ", warn.msg)
      return(invisible(0))
    }
    node.data=lapply(node.data, "[", sel.idx)
  } else {
    gR1=try(parseKGML2Graph2(xml.file[i], genes=F, expand=expand.node, split.group=split.group), silent=T)
    node.data=try(node.info(gR1), silent=T)
    if(class(node.data)[1]=="try-error"){
      warn.msg=sprintf(warn.fmt, xml.file[i])
      message("Warning: ", warn.msg)
      return(invisible(0))
    }
  }


  if(species=="ko") gene.node.type="ortholog" else gene.node.type="gene"
  if((!is.null(gene.data) |map.null) & sum(node.data$type==gene.node.type)>1){
    plot.data.gene=node.map(gene.data, node.data, node.types=gene.node.type, node.sum=node.sum, entrez.gnodes=entrez.gnodes)
    kng=plot.data.gene$kegg.names
    kng.char=gsub("[0-9]", "", unlist(kng))
    if(any(kng.char>"")) entrez.gnodes=FALSE
    if(map.symbol & species!="ko" & entrez.gnodes) {
              if(is.na(gene.annotpkg)) {
                warn.fmt="No annotation package for the species %s, gene symbols not mapped!"
                warn.msg=sprintf(warn.fmt, species)
                message("Warning: ", warn.msg)
              } else {
#                browser()
                plot.data.gene$labels=eg2id(as.character(plot.data.gene$kegg.names), category="SYMBOL", pkg.name=gene.annotpkg)[,2]
                mapped.gnodes=rownames(plot.data.gene)
                node.data$labels[mapped.gnodes]=plot.data.gene$labels
              }
            }
            cols.ts.gene=node.color(plot.data.gene, limit$gene, bins$gene, both.dirs=both.dirs$gene, trans.fun=trans.fun$gene, discrete=discrete$gene, low=low$gene, mid=mid$gene, high=high$gene,  na.col=na.col)
          } else plot.data.gene=cols.ts.gene=NULL
          if((!is.null(cpd.data) | map.null) & sum(node.data$type=="compound")>1){
#          if(sum(node.data$type=="compound")>1){
            plot.data.cpd=node.map(cpd.data, node.data, node.types="compound", node.sum=node.sum)
            if(map.cpdname & !kegg.native) { #@
              plot.data.cpd$labels=cpdkegg2name(plot.data.cpd$labels)[,2]
              mapped.cnodes=rownames(plot.data.cpd)
              node.data$labels[mapped.cnodes]=plot.data.cpd$labels
            }
            cols.ts.cpd=node.color(plot.data.cpd, limit$cpd, bins$cpd, both.dirs=both.dirs$cpd, trans.fun=trans.fun$cpd, discrete=discrete$cpd, low=low$cpd, mid=mid$cpd, high=high$cpd, na.col=na.col)
          } else plot.data.cpd=cols.ts.cpd=NULL

  if(kegg.native){
 pv.pars= keggview.native(plot.data.gene=plot.data.gene, cols.ts.gene=cols.ts.gene, plot.data.cpd=plot.data.cpd, cols.ts.cpd=cols.ts.cpd, node.data=node.data, pathway.name=pathway.name[i], kegg.dir=kegg.dir, limit=limit, bins=bins, both.dirs=both.dirs,discrete=discrete, low=low, mid=mid, high=high, na.col=na.col, ...)
} else{
  pv.pars= keggview.graph(plot.data.gene=plot.data.gene, cols.ts.gene=cols.ts.gene, plot.data.cpd=plot.data.cpd, cols.ts.cpd=cols.ts.cpd, node.data=node.data, path.graph=gR1, pathway.name=pathway.name[i],  map.cpdname=map.cpdname, split.group=split.group, limit=limit, bins=bins, both.dirs=both.dirs, discrete=discrete, low=low, mid=mid, high=high, na.col=na.col, ...)
}
  
  plot.data.gene=cbind(plot.data.gene, cols.ts.gene)
  if(!is.null(plot.data.gene)){
    cnames=colnames(plot.data.gene)[-(1:8)]
    nsamp=length(cnames)/2
    if(nsamp>1){
      cnames[(nsamp+1):(2*nsamp)]=paste(cnames[(nsamp+1):(2*nsamp)], "col", sep=".")
    } else cnames[2]="mol.col"
    colnames(plot.data.gene)[-(1:8)]=cnames
  }
  plot.data.cpd=cbind(plot.data.cpd, cols.ts.cpd)    
  if(!is.null(plot.data.cpd)){
    cnames=colnames(plot.data.cpd)[-(1:8)]
    nsamp=length(cnames)/2
    if(nsamp>1){
      cnames[(nsamp+1):(2*nsamp)]=paste(cnames[(nsamp+1):(2*nsamp)], "col", sep=".")
    } else cnames[2]="mol.col"
    colnames(plot.data.cpd)[-(1:8)]=cnames
  }
#  return(list(plot.data.gene=plot.data.gene, plot.data.cpd=plot.data.cpd))#out.list[[i]]=
  out.list[[i]]=list(plot.data.gene=plot.data.gene, plot.data.cpd=plot.data.cpd)
}

  if(npath==1) out.list=out.list[[1]] else names(out.list)=pathway.name
  
  return(invisible(out.list))
}