[BioC] bug in rendering reciprocal edges?

[Wouter van Atteveldt]

Thanks, I can confirm that this solved the problem.

> 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

summary: first call layoutGraph, then adjust the renderinfo..

BTW I found it quite difficult to figure out what function should be called when and with which arguments. Some options need to be given using the renderinfo, some using the attrs, and some using global options. The "new interface" pdf file is helpful but is more a tutorial than a reference... 

Thanks for solving my problem!

-- Wouter

On Tuesday, August 30, 2011 01:25:49 Nishant Gopalakrishnan wrote:
> Hi Wouter,
> 
> 
> 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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