CODEWITHSUNDEEP
rigraph
Piotr Wilczek
Piotr Wilczek

Reputation: 197

The plotting function in R igraph

I use igraph R to visualize chemical compounds. In this approach, nodes correspond to atoms and edges correspond to bonds between atoms. Such represented chemical molecule is known as a molecular graph or H-depleted graphs. For instance, to represent 2-methylbutane, 2mb for short, (simple organic molecule whose carbon skeleton consists of five atoms) I use the following R code: 

molecular.graph.2mb = graph.formula(1-2,2-3,3-4,2-5)

To visualize this molecular graph I use as a layout the following matrix m: 

m = matrix(c(1,0,2,0,3,0,4,0,2,1), nrow=5, byrow=TRUE).

This matrix contains coordinates of vertices of my graph. Then I plot this graph:

plot(molecular.graph.2mb, layout=m).

I obtain the graph where the geometrical distance between the vertices 2 and 5 is larger than between v1 and v2, v2 and v3 as well as v3 and v4.

My question is: How to force igraph R to plot the graph where all geometrical distances will be equal?

Upvotes: 1

Views: 255

Answers (1)

G5W
G5W

Reputation: 37641

The main trick to doing this is to set the parameter rescale=FALSE and adjust the xlim. Doing that alone made the nodes very small so I needed to adjust the node size as well. I think this is what you are looking for. 

library(igraph)

## Your graph
molecular.graph.2mb = graph.formula(1-2,2-3,3-4,2-5)
m = matrix(c(1,0,2,0,3,0,4,0,2,1), nrow=5, byrow=TRUE)

## Modified plot
plot(molecular.graph.2mb, layout=m, rescale=FALSE,
    vertex.size=30, xlim=c(0.5,4.5))

Evenly spaced

Upvotes: 1

Related Questions