rigraphsocial-networking

Odd edge behavior in `qgraph` after scaling node size with an attribute

[[Reproducible data for this question is found at bottom of question.]]

When plotting a network with qgraph, the edges usually link to nodes in a relatively straightforward way.

library(qgraph)
qgraph(Network)

enter image description here

But as soon as I add a size to my nodes, the edges often overshoot the nodes:

qgraph(Network,
       vsize=log(Attributes)*3, # scale nodes
       vTrans=150, #Transparency of the nodes
       label.scale=F # don't scale labels along with nodes
 )

enter image description here

Some node scaling sizes work better than others:

qgraph(Network,vsize=Attributes/5,
       vTrans=150,#Transparency of the nodes, must be an integer between 0 and 255, 255 indicating no transparency
       label.scale=F)

enter image description here

But it isn't clear why this is the case, or how I can override the edges to meet the node appropriately (either at the boundary of the scaled node or at the centerpoint of the node). Any thoughts welcome.

Data:

Network<-structure(list(V4 = c(0, 0, 0.6, 0.01, 0.06, 0.09, 0.01, 0.01, 
0, 0.01, 0.03, 0, 0, 0, 0.12, 0.04, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V5 = c(0, 0, 0.6, 
0.01, 0.06, 0.09, 0.01, 0.01, 0, 0.01, 0.03, 0, 0, 0, 0.13, 0.04, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V6 = c(0, 0, 0, 0.02, 0.12, 0.08, 0, 0.01, 0, 0.01, 0.02, 
0, 0, 0, 0.04, 0.02, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0), V7 = c(0, 0, 0, 0, 0, 0, 0.01, 0.01, 
0.01, 0.03, 0.01, 0.03, 0.05, 0, 0.03, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0.01, 0, 0, 0), V8 = c(0, 
0, 0, 0, 0, 0, 0.01, 0.01, 0.01, 0.03, 0.01, 0.03, 0.06, 0, 0.03, 
0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 
0, 0.01, 0, 0, 0), V9 = c(0, 0, 0, 0, 0, 0, 0.01, 0.01, 0.01, 
0.03, 0.01, 0.03, 0.01, 0, 0.04, 0.02, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0.01, 0, 0, 0), V10 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0.01, 0.01, 0.01, 0.04, 0.05, 0, 0.01, 0, 
0.02, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0.01, 0, 0, 0, 
0, 0.01, 0, 0, 0), V11 = c(0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0.01, 
0.01, 0.03, 0.08, 0, 0, 0, 0.02, 0, 0.02, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0.01, 0, 0, 0), V12 = c(0, 0, 0, 
0, 0, 0, 0, 0, 0, 0.01, 0, 0.07, 0, 0, 0, 0, 0.01, 0, 0.02, 0, 
0.02, 0.01, 0.01, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.02, 0.01, 0, 0, 0.01, 
0, 0, 0, 0, 0), V13 = c(0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0.01, 
0.04, 0.05, 0, 0, 0, 0.02, 0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0.01, 0.01, 0, 0, 0, 0, 0.01, 0, 0, 0), V14 = c(0, 0, 
0, 0, 0, 0, 0, 0.01, 0.01, 0.02, 0, 0.01, 0.09, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), V15 = c(0, 0, 0, 0, 0, 0, 0, 0.01, 0.01, 0.02, 0, 0, 0.09, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0), V16 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0), V17 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0.21, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0), V18 = c(0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0.02, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0), V19 = c(0, 0, 0, 0, 0, 0, 0, 
0, 0.01, 0.01, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0.01, 0, 0.01, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.02, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0), V20 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0.01, 0, 0, 0.08, 0, 
0.01, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0), V21 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0.07, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V22 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 
0, 0.01, 0.01, 0.09, 0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0), V23 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0.01, 0, 0, 0, 0, 0, 0.01, 0.01, 0.09, 0, 0.01, 0, 0.01, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V24 = c(0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0.01, 0.01, 0.09, 
0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V25 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 
0, 0.01, 0.01, 0.09, 0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0), V26 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0.01, 0, 0, 0, 0, 0, 0.01, 0.01, 0.09, 0, 0.01, 0, 0.01, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V27 = c(0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0.01, 0.01, 0.09, 
0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V28 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 
0, 0.01, 0.01, 0.09, 0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0), V29 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.01, 0, 0, 0, 0, 0, 0.01, 0, 0.05, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V30 = c(0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0.01, 0.01, 0.09, 0, 0.01, 0, 
0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V31 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0.01, 0.01, 0.09, 
0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V32 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.07, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.03, 0, 0, 0, 0, 0, 
0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0), V33 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0.02, 0.02, 0, 0, 0.01, 0.01, 0.01, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V34 = c(0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0.03, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V35 = c(0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0.03, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V36 = c(0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0.03, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V37 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V38 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V39 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V40 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.02, 0, 0, 0.01, 
0.01, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), V41 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0), V42 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 
0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V43 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0), V44 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0.06, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0), V45 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0.01, 0, 0, 0.01, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0), V46 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0.02, 0.07, 0.02, 0, 0, 0.01, 0, 0.01, 0, 0, 0.01, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V47 = c(0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V48 = c(0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.04, 0, 0.01, 0.01, 0.01, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V49 = c(0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0.01, 0, 0, 0.01, 
0.01, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), V50 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.02, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0), V51 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0.01, 0.03, 0.01, 0, 0, 0.01, 0.01, 0.01, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0), V52 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0.02, 0.01, 0.03, 0, 0.01, 0.02, 0.02, 0.02, 
0.02, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V53 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.09, 0, 
0.06, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V54 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 
0, 0, 0, 0.01, 0.01, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0, 0.01, 
0.09, 0, 0.01, 0, 0, 0, 0.02, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 
0, 0, 0, 0, 0), V55 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0.01, 0.01, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.08, 0, 0, 0, 0, 0, 0.02, 0, 0, 0, 0, 0, 
0.01, 0, 0, 0, 0, 0.02, 0, 0, 0, 0), V56 = c(0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.05, 0.08, 0, 0.02, 0, 0, 0.01, 
0.01, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), V57 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0.01, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0.01, 0.02, 0.03, 0, 0.01, 
0), V58 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 
0, 0.08, 0, 0, 0, 0, 0, 0.03, 0.01, 0.01, 0.01, 0.01, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0), V59 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0.03, 0, 0, 0, 0, 0, 0.03, 0, 0, 0.01, 0.01, 
0, 0, 0, 0, 0, 0.02, 0, 0.02, 0, 0, 0), V60 = c(0, 0, 0, 0, 0, 
0, 0, 0, 0.01, 0.02, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.02, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.02, 0.04, 0, 0, 0, 0), V61 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.01, 0, 0, 0, 0, 0, 0, 0), V62 = c(0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.06, 0.04, 0.01, 0, 0), 
    V63 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0.03, 0.01, 0, 0, 0)), class = "data.frame", row.names = c("4", 
"5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", 
"16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", 
"27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", 
"38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", 
"49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", 
"60", "61", "62", "63"))

Attributes<-c(34.93768692, 4.75733614, 13.93967533, 2.833557367, 8.325469971, 
              8.177970886, 2.928951502, 2.174068213, 7.494392872, 6.128136158, 
              2.818100929, 1.909636378, 3.748121262, 1e-05, 70.72342682, 22.41350937, 
              2.115944386, 0.005, 1.84581995, 0.102126002, 15.20289135, 2.613022089, 
              4.338716984, 0.032485999, 0.059714999, 0.080463, 0.035101, 0.011345, 
              1, 3.151705027, 0.239722997, 0.137802005, 0.017914001, 0.036782667, 
              1.388822675, 0.435640007, 3.397774458, 2.329986095, 21.80796051, 
              0.200000003, 1.358244658, 0.687838018, 2.832928419, 1.016921043, 
              11.10915184, 2.84529686, 0.925952315, 4.18819809, 3.080216408, 
              0.276921213, 1.808943033, 3.043907881, 0.426636606, 80, 3.872853518, 
              7.236839294, 1.322934866, 11.1804142, 3.803627491, 31.66708755
)
Solution

  • The edges aren't necessarily wrong. You've given many of the nodes negative values. if you even set them to 1, the arrows do as you expect. For example, vsize = ifelse(log(Attributes) * 3 > 0, log(Attributes) * 3, 1) will present with all meaningful arrows.

    I'm surprised it didn't cause an error when you made the nodes negative... it's actually really nice that it didn't. It probably made it a lot easier to figure out what was wrong. When you used Attributes/5 you didn't end up with negative values.