R/showSigNodes.R

In GOFunction: GO-function: deriving biologcially relevant functions from statistically significant functions

showSigNodes <-
function(DAG, sigTerm, sigTerm_Local, sigTerm_Global, dagTermInfo, bmpSize, filename) {

  require('Rgraphviz') || stop('package Rgraphviz is required')

  graphAttrs <- getDefaultAttrs(layoutType = 'dot')
  graphAttrs$cluster <- NULL
  graphAttrs$node$shape <- 'ellipse'
  graphAttrs$node$fontsize <- '20'
  
  nodeAttrs <- list()
  edgeAttrs <- list()
  
  allTerm <- as.character(dagTermInfo[,1])
  nodeAttrs$label[allTerm] <- allTerm
  

  rmLocalTerm <- setdiff(sigTerm, sigTerm_Local)
  nodeAttrs$color[rmLocalTerm] <- rep('red', length(rmLocalTerm))
  nodeAttrs$shape[rmLocalTerm] <- rep('circle', length(rmLocalTerm))

  rmGlobalTerm <- setdiff(sigTerm_Local, sigTerm_Global)
  nodeAttrs$color[rmGlobalTerm] <- rep('red', length(rmGlobalTerm))
  nodeAttrs$shape[rmGlobalTerm] <- rep('box', length(rmGlobalTerm))
  nodeAttrs$height[rmGlobalTerm] <- rep('0.7', length(rmGlobalTerm))
  nodeAttrs$width[rmGlobalTerm] <- rep('0.7', length(rmGlobalTerm))

  nodeAttrs$color[sigTerm_Global] <- rep('red', length(sigTerm_Global))
  nodeAttrs$shape[sigTerm_Global] <- rep('rectangle', length(sigTerm_Global))
  nodeAttrs$height[sigTerm_Global] <- rep('0.7', length(sigTerm_Global))
  nodeAttrs$width[sigTerm_Global] <- rep('1.1', length(sigTerm_Global))



  dagTermInfo[dagTermInfo[,5]<2.2E-16,5] <- 2.2E-16;
  dagTermInfo[dagTermInfo[,6]<2.2E-16,6] <- 2.2E-16;
  dagTermInfo$colorran <- round(log10(dagTermInfo[,6])-range(log10(dagTermInfo[,6]))[1] + 1)
  mm <- max(dagTermInfo$colorran)
  colorMap <- heat.colors(mm)
  nodeAttrs$fillcolor[allTerm] <- unlist(lapply(dagTermInfo$colorran, function(x) return(colorMap[x])))
  
  weightsList <- edgeWeights(DAG)
  to <- lapply(weightsList, names)
  from <- nodes(DAG)
  edge.names <- paste(rep(from, listLen(to)), unlist(to), sep = "~")
  edge.weights <- unlist(weightsList)
  names(edge.weights) <- edge.names
  ##    0 for a is_a relation,  1 for a part_of relation
  edgeAttrs$color <- ifelse(edge.weights == 0, 'black', 'red')
  filename <- paste(filename,".bmp",sep="")
  bmp(filename, width = bmpSize, height = bmpSize, res = 300, antialias = "none");
  plot(DAG, attrs = graphAttrs, nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs)  
  dev.off()
}