how to fix the strange edge, like -|, rather than ->?

Usage
1

I am struggling to fix strange edges in my plot.

plot(tg,
     vertex.size=5+abs(tg0.pr$vector)*200,
     vertex.label.cex=.7,
     edge.arrow.size=0.00001,
     edge.arrow.width=0.00001,
     vertex.label=V(tg)$names,
     vertex.color=V(tg)$color,
     vertex.label.color="black",
     edge.curved=0.2,
     edge.color="gray50",
     layout=layout_nicely(tg)
     )

results to

image
image1739×1703 228 KB

??? Can anyone help to sort this out?
Using the similar lines with different data I can produce normal arrow edges…
Many thanks!

2

Can you show a self-contained minimal example that would allow us to reproduce problem?

3

Many thanks, I append the simple code. Allow size is set very small, 0.00001, otherwise background becomes a gray plan… No idea why I am having this picture… L

rm(list = ls())
gc()

t0=matrix(c(5.217060,    0,    0,    0, 0.000000, 0.000000, 0.000000,    0,    0
,0.000000 ,   0 ,   0 ,   0, 0.000000, 0.000000 ,0.000000 ,   0 ,   0
,4.458724  ,  0  ,  0  ,  0, 0.000000, 4.434984 ,0.000000  ,  0  ,  0
,0.000000   , 0   , 0   , 0, 0.000000, 0.000000 ,0.000000   , 0   , 0
,0.000000    ,0 ,   0    ,0, 6.684027, 0.000000 ,0.000000,    0,    0
,0.000000,    0  ,  0 ,   0, 0.000000, 0.000000 ,0.000000 ,   0 ,   0
,0.000000 ,   0   , 0  ,  0 ,0.000000, 4.382870 ,6.358501  ,  0  ,  0
,0.000000  ,  0  ,  0   , 0, 0.000000, 0.000000 ,0.000000   , 0   , 0
,0.000000   , 0   , 0   , 0, 0.000000, 0.000000 ,0.000000   , 0    ,0),
9,9)

t=t(t0)
library(igraph)
M=unname(as.matrix(t))
tg=graph.adjacency(M) 
tg=delete.vertices(simplify(tg,remove.multiple=T,remove.loops=T),degree(tg)==0)

lay = layout_nicely(tg)

plot(tg,
     vertex.size=10,
     vertex.label.cex=.7,
     edge.arrow.size=0.00001,
     edge.arrow.width=0.00001,
     edge.curved=0.2,
     layout=lay
     )

image
image567×643 5.86 KB

4

I cannot reproduce the problem on macOS with R 4.1.1, igraph 1.2.9.

That said, why are you using such extreme value for arrowhead sizes? If you don’t want arrows, you can use edge.arrow.mode='-'.

5

Many thanks. I updated (windows 64bit) to R 4.1.2, igraph 1.2.8, and Rtool 4 but the problem persist.
restricting edge.arrow.mode works by putting ‘-’ works, but I would like to use arrows…
The reason why I use extreme values for arrowhead sizes are the following. if I used
edge.arrow.size=0.01,
edge.arrow.width=0.01,
then I get

image
image611×705 6.73 KB

L

6

I have tried to use a different PC and it worked. It might be related to something the R use to produce a graphic (PDF?). Many thanks to szhorvat. L

7

I’m sorry, this reaches the end of my knowledge.

If you have an example that does not use very extreme (large or small) values and produces unusual output, I suggest you file a bug report. Please make the example small, but complete. Include a command to export the graphics to a file (in case the issue is related to some specific graphics backend). Also include full details about your system (version, OS, etc.), just as you did here.

At the moment we are short on R experts, but the problem should at least be documented so it could be looked at later.