[igraph] misplaced edges in fixed layout

[Leroi, Armand M]

Hello,

I am using a fixed layout.  Under some circumstances, the behaviour of the edges appears to interact with vertex.size in an unfortunate way 

Below is an example.  Here, the default vertex size (15?) gives almost invisible vertices.  But the edges and arrow heads all line up nicely.  So, I increase the vertex.size = 300. Now they’re visible, however, some of the edges no longer run from vertex-to-vertex. They’re misplaced and pointing in the wrong direction.  This phenomenon seems to affect y-axis-stacked nodes most acutely.  Can anyone suggest a fix?  Below is a MWE.  Play around with vertex.size and you should see what I mean. 

With thanks

Armand

nodes <- c('a','b','c','d','e','f')

x <- c(1540, 1540, 1540,1580,1600,1650)

y <- c(52, 53, 55,56,54,58)

from <- c('a','a','a','a','e','d')

to <- c('b','c','d','e','f','f')

Nodelist <- data.frame(nodes, x ,y)

Edgelist <- data.frame(from, to)

a<- graph_from_data_frame(vertices = Nodelist, d= Edgelist, directed = TRUE)

plot(a, ylim=c(52,58), xlim=c(1530,1650), asp=0, rescale=FALSE, axes=TRUE, vertex.size=400)

smallnodes.pdf
Description: smallnodes.pdf

bignodes.pdf
Description: bignodes.pdf