Names drop in RBioFabric output

[Tom Roth]

Hi Bill

This'll probably be a quick fix. 

I have a dataset (call it d) structured like

  parent child

1      -     2

2  16710 15636

3  16951 15637

4  17514 15638

5  17515 15638

6  17163 15639

My dataset d has about four thousand rows, so it's not small. It doesn't represent directed data either. 

I convert d to igraph format using 

    g = graph_from_data_frame(d, directed = FALSE)

that converts it to a structure that looks like 

[1] -    --2     16710--15636 16951--15637 17514--15638 17515--15638

then run BioFabric like 

    height <- vcount(g) 

    width <- ecount(g)

    aspect <- height / width;

    plotWidth <- 10.0

    plotHeight <- plotWidth * (aspect * 1.2)

    pdf("myBioFabricOutput.pdf", width=plotWidth, height=plotHeight)

    bioFabric(g)

    dev.off()

The graph is output fine to the pdf document, except the only text label that appears is 2. No other label is displayed. 

What am I doing wrong? Should I be using the autoNameForFabric() function in there somewhere?

Cheers,

Tom  

[Bill Longabaugh]

If node zone labels get too tiny, I found that they can have trouble getting rendered. What happens if you increase the plot size? For big networks, you want to get crazy-big so you can get the resolution you need (e.g 50 inch PDFS or 30,000 pixel-wide PNGs).

Let me know how it goes.

Thanks for using BioFabric.

Bill