Project: s41467-024-46181-3 | Function: comparision.TSS.proximal.distall.mafb.gata3 (r)

system: You are an expert R programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow R best practices and maintain consistent code style.
Return **only** the complete R function code.

user: Complete this R function:

**DESCRIPTION:** Compare transcriptional start site (TSS) proximity for MAFB and GATA3 transcription factors. Implements comparative analysis of transcription factor binding relative to gene promoters.

**KEY TERMS:** {
  "TSS": "transcriptional start site",
  "proximal": "near promoter regions",
  "MAFB/GATA3": "transcription factors"
}

**CONTEXT CODE:** 
#R v.4
#enrichment comparison TSS-proximal vs TSS-distal for MAFB and GATA3
comparision.TSS.proximal.distall.mafb.gata3 <- function(){
  stop("Function implementation has been masked")
  # Compare TSS-proximal vs TSS-distal peaks for MAFB and GATA3.

#TF network plot
tf.network.plot<-function(){
  stop("Function implementation has been masked")
  # first we found TFs motifs at the GCM2 proximal regions (5kb window)
  # filter out silent genes in parathyroids or genes that are not associated with super-enhancers in parathyroids
  # For those genes, we made connections between genes and constructed network with nodes and links.
  # nodes and links for the tf network

  load("data/f3.data.RData")
  head(nodes)
  head(links)
  nrow(nodes); length(unique(nodes$id))
  nrow(links); nrow(unique(links[,c("from", "to")]))

  library(igraph);
  net <- graph.data.frame(links, nodes, directed=T)
  x11();plot(net, edge.arrow.size=.4,vertex.frame.color="#ffffff");
    plot(net, layout=layout_in_circle,arrow.size=.2,vertex.frame.color="#ffffff");
  V(net)$color=c("red","blue");
    plot(net, layout=layout_in_circle,arrow.size=.2,vertex.frame.color="#ffffff");

  #ordered by connectivity
  genes=nodes$id;
  names(genes)=genes;
  counts=unlist(lapply(genes,function(gene){
    sum(links$from==gene)+sum(links$to==gene)}))
  order(counts)
  nodes2=genes[rev(order(counts))][c(2,1,3:15)]
  net2 <- graph.data.frame(links, nodes2, directed=T)
  
  library(RColorBrewer)
  cols=rev(unlist(lapply(1:9,function(i) {col=brewer.pal(n=9, name="Oranges")[i];
                                   return(c(col,col))})));
  V(net2)$color=cols[3:17]
  col2=rep("white",times=15);
  auto=unlist(lapply(nodes2,function(gene){
    id=which(links$from==gene & links$to==gene)
    if(length(id)>0){return(gene)}}))
  ids=match(auto,nodes2);
  col2[ids]="black"
  id=which(nodes2=="GATA3");
  col2[id]=brewer.pal(n=9, name="YlGn")[5];
  x11();
plot(net2, vertex.size=30,layout=layout_in_circle,arrow.size=.2,vertex.frame.color=col2, vertex.label.color=c("black"),vertex.label.family="Helvetica")
}


Complete the function implementation replacing "stop("Not implemented")".