[BioC] fontsize in Rgraphviz

[Deepayan Sarkar]

On 1/29/08, Mark W Kimpel <mwkimpel at gmail.com> wrote:
> Deepayan,
>
> Thanks for your efforts, it looks like you are working on major changes
> to Rgraphviz for BioC 2.2.
>
> Your example worked for me (with R-devel), but I can't get my own
> function to work. Below is my code, or what I hope is the relevant part,
> with the error output. It looks to me like layoutGraph is looking for a
> way to render a "neato" graph and can't find it, but I'm probably wrong.
> It also looks to me like you are making some major changes to the way
> node and edge attributes are passed to the rendering engine, so maybe
> the parameters I used to pass to plot(my.graphNEL) are not working.
>
> Let me know what you think I am doing wrong. Mark

The error messages are not telling me much. Can you provide a
reproducible example (preferably something simple)?

-Deepayan

>
> [1] "created graphAM"
> [1] "created graphNEL"
> Error in layoutGraph(result.gN, layout.param, layoutfun = "dot",
> nodeAttrs = nAttrs,  :
>    could not find function "layoutFun"
>
> Enter a frame number, or 0 to exit
>
> 1: result.matrix.graph.func(result.matrix = cocite.mat.sig, no.edges =
> TRUE, m
> 2: switch(file.output, ps = {
> 3: layoutGraph(result.gN, layout.param, layoutfun = "dot", nodeAttrs =
> nAttrs,
>
> Selection:
>
>   #font size
>           if(file.output != "screen"){
>             #cex.vec <-floor(22 * nodeAttrs(result.gN)$nodeWidth)
>              cex.vec <- rep(48, length(nodes(result.gN)))
>           } else {cex.vec <-rep(18, length(nodeAttrs(result.gN)$nodeWidth))}
>           names(cex.vec) <- nodes(result.gN)
>
>           fileName<-paste(experiment, contrast, "FDR", FDR, "Graph",
> "ps", sep=".")
>           postscript(file=fileName, paper="special",width=width,
> height=height) #set up graphics device
>           x <- layoutGraph(result.gN, layout.param, layoutfun = "dot",
> nodeAttrs = nAttrs, edgeAttrs = eAttrs,
>                main=paste("Experiment:", experiment, ";  Contrast:",
> contrast,";  FDR:", FDR,
>                  ";Total Genes:", length(nodes(result.gN)), "; Total
> Connections:",
>                  round(aveNumEdges(result.gN)*length(nodes(result.gN)),
> digits=0),"; Min. connections ==",
>                  min.edges, "; Min. citations per connection ==",
> min.cites, "; Additional search criteria:",
>                  termAdditional, sep=" "))
>                   nodeRenderInfo(x) = list(fontsize = cex.vec)
>           renderGraph(x)
>           dev.off()## close the graphics device
>
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 204-4202 Home (no voice mail please)
>
> mwkimpel<at>gmail<dot>com
>
> ******************************************************************
>
>
> Deepayan Sarkar wrote:
> > On 1/25/08, Mark W Kimpel <mwkimpel at gmail.com> wrote:
> >> I would like to vary the font size of node labels in Rgraphviz as I have
> >> been varying node size by fold change magnitude. Unfortunately, many
> >> attempts have failed and I continue to get the same font size. Here is
> >> my code followed by sessionInfo()
> >>
> >> nAttrs$fontsize<-floor(22 * nodeWidth)
> >>
> >> nodeWidth is a vector of widths which vary by node according to fold
> >> change. This works nicely, but font size does not.
> >
> > We have been playing an alternative rendering interface. With
> > bioc-devel, I get varying node sizes and label size using
> >
> >
> > set.seed(123)
> > V <- letters[1:10]
> > M <- 1:4
> > g1 <- randomGraph(V, M, .2)
> >
> > cex.list <- runif(length(nodes(g1)))
> > names(cex.list) <- nodes(g1)
> >
> > width.list <- seq(0.2, 2, length = length(nodes(g1)))
> > names(width.list) <- nodes(g1)
> >
> > x <- layoutGraph(g1, nodeAttrs = list(width = width.list))
> > nodeRenderInfo(x) = list(fontsize = 50 * cex.list)
> > renderGraph(x)
> >
> >
> >
> > I'm not sure if this will work with Bioc 2.1.
> >
> > -Deepayan
> >
>