In spholmes/GraphsTutorial: Practical Tutorial on Graph Manipulation

library(learnr)
knitr::opts_chunk$set(echo = FALSE, message=FALSE, warning=FALSE)

Choices made by the plotting programs

Different graph layouts

Graph Layout

library("igraph")

In case you did not run the Creating Graphs tutorial, you can run the following code:

data(chemodats)
gr = graph_from_data_frame(chemodats[,c("node1", "node2")], directed = FALSE)
E(gr)$weight = 1
V(gr)$size = centralization.degree(gr)$res

If you look at the help for igraph.plotting you find a description of many different choices for laying out the graph as usually the x and y coordinates are not provided data but extra information that is only computed for aesthetic or clarity.

If you don't provide a layout all the graph plotting functions will pick one for your (very often a Fruchterman-Reingold) which tries to stretch the graph enough so that are not too many overlapping edges, a little like Multidimensional Scaling stretches the points out.

Let's look at some examples; these are all the same graphs but with different layout choices.

co <- layout_with_fr(gr)
## Fruchterman-Reingold layout (force directed layout)
plot(gr, layout=co)
## On a circle
coordsc <- layout_in_circle(gr)
plot(gr, layout=coordsc)
##The Kamada-Kawai layout algorithm
plot(gr, layout=layout_with_kk)

Try to find other layout choices (on a grid, on a sphere, through multidimensional scaling).

lgrid <- layout_on_grid(gr)
lmds <- layout_with_mds(gr)
lsphere <- layout_on_sphere(gr)

lmds <- layout_with_mds(gr)
lgrid <- layout_on_grid(gr)
lsphere <- layout_on_sphere(gr)
plot(gr, layout=lmds)
plot(gr,layout=lgrid)
plot(gr, layout=lsphere)

Quiz

Some questions to verify that you understand the way we use graphs:

quiz(
  question("Which package contains functions for plotting graphs?",
    answer("base"),
    answer("graph"),
    answer("igraph", correct = TRUE),
    answer("codetools")
  ),
  question("Which of the objects listed below are components of a graph?",
    answer("vertex", correct = TRUE),
    answer("border"),
    answer("center"),
    answer("edge", correct = TRUE)
  )
)