[BioC] bug in rendering reciprocal edges?

[Nishant Gopalakrishnan]

Hi Wouter,

Please change the position of the call to the layoutGraph function in 
your render function as follows and you shall see the reciprocal edges 
with color and line width

render <- function(graph) {
   nodes = union(graph$subject, graph$object)
   edges = tapply(graph$object, graph$subject, function(x) 
list(edges=as.character(x)), simplify=F)
   # add edges for object-only nodes (leafs)
   for (leaf in setdiff(graph$object, graph$subject)) edges[[leaf]] = 
list(edges=NULL)
   # create graph
   g <- new("graphNEL", nodes = nodes, edgeL = edges, edgemode="directed")
   # add labels, width, color if given

   edgeids = paste(graph$subject, graph$object, sep="~")
   edgeAttrs = if (is.null(graph$label)) list() else
     list(label=namedvector(edgeids, as.character(graph$label)) )
   ## layout
   g = layoutGraph(g, recipEdges="distinct", edgeAttrs=edgeAttrs)

   if (!is.null(graph$col))
     edgeRenderInfo(g) <- list(col=namedvector(edgeids, 
as.character(graph$col)))
   if (!is.null(graph$width))
     edgeRenderInfo(g) <-  list(lwd=namedvector(edgeids, graph$width))
   if (!is.null(graph$label))
     edgeRenderInfo(g) <- list(label=namedvector(edgeids, 
as.character(graph$label)))
   #render
   renderGraph(g)
}


Nishant


On 08/29/2011 09:55 AM, Wouter van Atteveldt wrote:
> Dear list,
>
> I want to use RGraphviz to create network diagrams of relations between actors (eg a social network), using attributes such as label, colour, and width to visualize relationship strength and valence.
>
> I decided to create a little helper function that takes a data frame of subject, object and optional width, label, and colour and renders that as a graph using Rgraphviz. This works fine, also for moderately complex graphs. However, reciprocal edges seem to give problems if colour and line width are used.
>
> Below is included a small test program that creates two sets of graphs, varying on including a reciprocal and on the amount of 'features' (label, colour etc). (Syntax highlighted version at http://pastebin.com/bQGgaDiT).
>
> Resulting picture available at http://imageshack.us/photo/my-images/405/recip.png/ . You can see that the top row renders fine, but in the bottom row (which has a reciprocal relation) the relation from b to a loses its arrowhead when linewidths are added and disappears altogether (except for its label) when color is added.
>
> I am using R version 2.12.1 (2010-12-16), Platform: x86_64-pc-linux-gnu (64-bit), Rgraphviz 1.28.0. I tried both RStudio and 'vanilla' R.
>
> Thanks,
>
> ---------
>
> library(Rgraphviz)
>
> # Assumes that a graph is  a data frame with columns
> # subject, object, [label, width, hue, saturation, brightness]
>
> namedvector<- function(names, values) {names(values) = names; values}
>
> render<- function(graph) {
>    nodes = union(graph$subject, graph$object)
>    edges = tapply(graph$object, graph$subject, function(x) list(edges=as.character(x)), simplify=F)
>    # add edges for object-only nodes (leafs)
>    for (leaf in setdiff(graph$object, graph$subject)) edges[[leaf]] = list(edges=NULL)
>    # create graph
>    g<- new("graphNEL", nodes = nodes, edgeL = edges, edgemode="directed")
>    # add labels, width, color if given
>    edgeids = paste(graph$subject, graph$object, sep="~")
>    edgeAttrs = if (is.null(graph$label)) list() else
>      list(label=namedvector(edgeids, as.character(graph$label)) )
>    if (!is.null(graph$col))
>      edgeRenderInfo(g)<- list(col=namedvector(edgeids, as.character(graph$col)))
>    if (!is.null(graph$width))
>      edgeRenderInfo(g)<-  list(lwd=namedvector(edgeids, graph$width))
>    if (!is.null(graph$label))
>      edgeRenderInfo(g)<- list(label=namedvector(edgeids, as.character(graph$label)))
>    # layour and render
>    g = layoutGraph(g, recipEdges="distinct", edgeAttrs=edgeAttrs)
>    renderGraph(g)
> }
>
> # test code: create normal and reciprocal graph and some attributes
> graph = data.frame(subject=c("a", "c"), object=c("a", "a"))
> rgraph = data.frame(subject=c("a", "b"), object=c("b", "a"))
> label=c("0.7","-1.0")
> col=c("blue","red")
> width=c(2,4)
>
> # plot graphs in rows with increasing #features complexity in columns
> layout(matrix(1:8, nrow=2, byrow=T))
> for (g in list(graph, rgraph)) {
>    render(g)
>    render(cbind(g, label=label))
>    render(cbind(g, label=label, width=width))
>    render(cbind(g, label=label, width=width, col=col))
> }
>
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