R/exportFunctions.R

In milescsmith/WGCNA: Weighted Correlation Network Analysis

# Functions for exporting networks to various network visualization software

exportNetworkToVisANT <- function(
                                  adjMat,
                                  file = NULL,
                                  weighted = TRUE,
                                  threshold = 0.5,
                                  maxNConnections = NULL,
                                  probeToGene = NULL) {
  adjMat <- as.matrix(adjMat)
  adjMat[is.na(adjMat)] <- 0
  nRow <- nrow(adjMat)
  checkAdjMat(adjMat, min = -1, max = 1)
  probes <- dimnames(adjMat)[[1]]
  if (!is.null(probeToGene)) {
    probes2genes <- match(probes, probeToGene[, 1])
    if (sum(is.na(probes2genes)) > 0) {
      stop("Error translating probe names to gene names: some probe names could not be translated.")
    }
    probes <- probeToGene[probes2genes, 2]
  }

  rowMat <- matrix(c(1:nRow), nRow, nRow, byrow = TRUE)
  colMat <- matrix(c(1:nRow), nRow, nRow)

  adjDst <- as.dist(adjMat)
  dstRows <- as.dist(rowMat)
  dstCols <- as.dist(colMat)

  if (is.null(maxNConnections)) maxNConnections <- length(adjDst)

  ranks <- rank(-abs(adjDst), na.last = TRUE, ties.method = "first")
  edges <- abs(adjDst) > threshold & ranks <= maxNConnections
  nEdges <- sum(edges)

  visAntData <- data.frame(
    from = probes[dstRows[edges]],
    to = probes[dstCols[edges]],
    direction = rep(0, nEdges),
    method = rep("M0039", nEdges),
    weight = if (weighted) adjDst[edges] else rep(1, nEdges)
  )

  if (!is.null(file)) {
    write.table(visAntData, file = file, quote = FALSE, row.names = FALSE, col.names = FALSE)
  }

  invisible(visAntData)
}

exportNetworkToCytoscape <- function(
                                     adjMat,
                                     edgeFile = NULL,
                                     nodeFile = NULL,
                                     weighted = TRUE,
                                     threshold = 0.5,
                                     nodeNames = NULL,
                                     altNodeNames = NULL,
                                     nodeAttr = NULL,
                                     includeColNames = TRUE) {
  adjMat <- as.matrix(adjMat)
  adjMat[is.na(adjMat)] <- 0
  nRow <- nrow(adjMat)
  checkAdjMat(adjMat, min = -1, max = 1)
  if (is.null(nodeNames)) nodeNames <- dimnames(adjMat)[[1]]
  if (is.null(nodeNames)) {
    stop("Cannot determine node names: nodeNames is NULL and adjMat has no dimnames.")
  }
  rowMat <- matrix(c(1:nRow), nRow, nRow, byrow = TRUE)
  colMat <- matrix(c(1:nRow), nRow, nRow)

  if (!is.null(nodeAttr)) {
    if (is.null(dim(nodeAttr))) nodeAttr <- data.frame(nodeAttribute = nodeAttr)
    nodeAttr <- as.data.frame(nodeAttr)
  } else {
    nodeAttr <- data.frame(nodeAttribute = rep(NA, ncol(adjMat)))
  }


  adjDst <- as.dist(adjMat)
  dstRows <- as.dist(rowMat)
  dstCols <- as.dist(colMat)

  edges <- abs(adjDst) > threshold
  nEdges <- sum(edges)
  edgeData <- data.frame(
    fromNode = nodeNames[dstRows[edges]],
    toNode = nodeNames[dstCols[edges]],
    weight = if (weighted) adjDst[edges] else rep(1, nEdges),
    direction = rep("undirected", nEdges),
    fromAltName = if (is.null(altNodeNames)) rep("NA", nEdges) else altNodeNames[dstRows[edges]],
    toAltName = if (is.null(altNodeNames)) rep("NA", nEdges) else altNodeNames[dstCols[edges]]
  )

  nodesPresent <- rep(FALSE, ncol(adjMat))
  nodesPresent[dstRows[edges]] <- TRUE
  nodesPresent[dstCols[edges]] <- TRUE
  nNodes <- sum(nodesPresent)
  nodeData <- data.frame(
    nodeName = nodeNames[nodesPresent],
    altName = if (is.null(altNodeNames)) rep("NA", nNodes) else altNodeNames[nodesPresent],
    nodeAttr[nodesPresent, ]
  )

  if (!is.null(edgeFile)) {
    write.table(edgeData,
      file = edgeFile, quote = FALSE, row.names = FALSE, col.names = includeColNames,
      sep = "\t"
    )
  }

  if (!is.null(nodeFile)) {
    write.table(nodeData,
      file = nodeFile, quote = FALSE, row.names = FALSE, col.names = includeColNames,
      sep = "\t"
    )
  }

  list(edgeData = edgeData, nodeData = nodeData)
}