Re: [igraph] Questions about walktrap.community

[Gábor Csárdi]

Hmmm, as.hclust.dendrogram requires integers as node ids, quite
strange, since this is usually not done in R. I have fixed this in the
0.5 development tree. Here is the new version of the as.dendrogram
function for walktrap objects. You can just redefine this in your
code. Please tell me if there are any more problems.

Btw. similar fixed were needed for as.dendrogram versions operating on
the output of edge-betweenness based and leading eigenvector based
community detection.

Best,
Gabor

########################

as.dendrogram.igraph.walktrap <- function (object, hang=-1,
                                           use.modularity=FALSE, ...)
{
  stopifnot(nrow(object$merges)> 0)
  storage.mode(object$merges) <- "integer"
  object$merges <- object$merges + 1L
  if (is.null(object$labels))
    object$labels <- 1:(nrow(object$merges)+1)-1
  z <- list()
  if (!use.modularity || is.null(object$modularity)) {
    object$height <- 1:nrow(object$merges)
  } else {
    object$height <- object$modularity[-1]
    object$height <- cumsum(object$height - min(object$height))
  }
  nMerge <- length(oHgt <- object$height)
  if (nMerge != nrow(object$merges))
    stop("'merge' and 'height' do not fit!")
  hMax <- oHgt[nMerge]
  one <- 1:1;
  two <- 2:2 # integer!
  leafs <- nrow(object$merges)+1
  for (k in 1:nMerge) {
    x <- object$merges[k, ]# no sort() anymore!
    if (any(neg <- x < leafs+1))
      h0 <- if (hang < 0) 0 else max(0, oHgt[k] - hang * hMax)
    if (all(neg)) {                  # two leaves
      zk <- as.list(x)
      attr(zk, "members") <- two
      attr(zk, "midpoint") <- 0.5 # mean( c(0,1) )
      objlabels <- object$labels[x]
      attr(zk[[1]], "label") <- objlabels[1]
      attr(zk[[2]], "label") <- objlabels[2]
      attr(zk[[1]], "members") <- attr(zk[[2]], "members") <- one
      attr(zk[[1]], "height") <- attr(zk[[2]], "height") <- h0
      attr(zk[[1]], "leaf") <- attr(zk[[2]], "leaf") <- TRUE
    }
    else if (any(neg)) {            # one leaf, one node
      X <- as.character(x)
      ## Originally had "x <- sort(..) above => leaf always left, x[1];
      ## don't want to assume this
      isL <- x[1] < leafs+1 ## is leaf left?
      zk <-
        if(isL) list(x[1], z[[X[2]]])
        else    list(z[[X[1]]], x[2])
      attr(zk, "members") <- attr(z[[X[1 + isL]]], "members") + one
      attr(zk, "midpoint") <-
        (igraph:::.memberDend(zk[[1]]) + attr(z[[X[1 + isL]]], "midpoint"))/2
      attr(zk[[2 - isL]], "members") <- one
      attr(zk[[2 - isL]], "height") <- h0
      attr(zk[[2 - isL]], "label") <- object$labels[x[2 - isL]]
      attr(zk[[2 - isL]], "leaf") <- TRUE
      }
    else {                        # two nodes
      x <- as.character(x)
      zk <- list(z[[x[1]]], z[[x[2]]])
      attr(zk, "members") <- attr(z[[x[1]]], "members") +
        attr(z[[x[2]]], "members")
      attr(zk, "midpoint") <- (attr(z[[x[1]]], "members") +
                               attr(z[[x[1]]], "midpoint") +
                               attr(z[[x[2]]], "midpoint"))/2
    }
    attr(zk, "height") <- oHgt[k]
    z[[k <- as.character(k+leafs)]] <- zk
  }
  z <- z[[k]]
  class(z) <- "dendrogram"
  z
}




On Fri, Oct 28, 2011 at 6:19 PM, Wang, Jing <address@hidden> wrote:
> Dear Gabor,
>
>        I can transform the walktrap data to dendrogram using as.dendrogram, 
> but
> when I transform the dendrogram to hclust type (because some functions
> need hclust type, so I must get the hclust data), I always get the
> following error:
>
>        Error: all(vapply(s, is.integer, NA)) is not TRUE
>
> So, would you please give me some suggestion how to address this error?
> Thank you very much for you help!
>
> Best,
> Jing
>
> On 10/28/11 3:36 PM, "Gábor Csárdi" <address@hidden> wrote:
>
>>On Fri, Oct 28, 2011 at 6:53 AM, Tamas Nepusz <address@hidden> wrote:
>>[...]
>>>> I have two questions about walktrap.community. The first question is
>>>>whether
>>>> there is a method to change the result of walktrap.community to a
>>>>"hclust"
>>>> class.
>>> I'm not an expert in the R interface so I cannot answer this question
>>>-- but
>>> maybe someone else on this list can.
>>
>>You can convert it to a 'dendogram' object, which you can simply plot
>>via 'plot()'. Just call 'as.dendrogram()' on it.
>>
>>G.
>>
>>[...]
>>
>>--
>>Gabor Csardi <address@hidden>     MTA KFKI RMKI
>>
>>_______________________________________________
>>igraph-help mailing list
>>address@hidden
>>https://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help
>



-- 
Gabor Csardi <address@hidden>     MTA KFKI RMKI