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Positioning the nodes of a graph

asked 2020-12-16 11:52:25 +0200

Cyrille gravatar image

updated 2020-12-16 17:31:19 +0200

slelievre gravatar image

This is a nbot easy readable graph. How can I reposition the nodes

A= matrix([
[1 , 1 , 0 , 1 , 0 , 0 , 0 , 0 , 0],
[1 , 1 , 1 , 0 , 1 , 0 , 0 , 0 , 0],
[0 , 1 , 1 , 0 , 0 , 1 , 0 , 0 , 0],
[1 , 0 , 0 , 1 , 1 , 0 , 1 , 0 , 0],
[1 , 0 , 0 , 1 , 1 , 0 , 1 , 1 , 0],
[0 , 1 , 0 , 1 , 1 , 1 , 0 , 1 , 0],
[0 , 0 , 1 , 0 , 1 , 1 , 0 , 0 , 1],
[0 , 0 , 0 , 1 , 0 , 0 , 1 , 1 , 0],
[0 , 0 , 0 , 0 , 1 , 0 , 1 , 1 , 1],
[0 , 0 , 0 , 0 , 0 , 1 , 0 , 1 , 1]])

D = DiGraph(A, format='adjacency_matrix')
D.show()

The node shoud be

                           1 2 3
                           4 5 6
                           7 8 9

Incidently I would like to know how to change the colors of the nodes, their sizes, the number of the nodes and the arcs.

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Comments

1

Read the documentation ?

FrédéricC gravatar imageFrédéricC ( 2020-12-16 12:04:22 +0200 )edit

The matrix has 10 rows and 9 columns. How is it a graph adjacency matrix?

slelievre gravatar imageslelievre ( 2020-12-16 16:00:47 +0200 )edit

Let us deal with node positions here, and with customising the nodes and arcs at the follow-up:

slelievre gravatar imageslelievre ( 2020-12-17 23:36:27 +0200 )edit

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answered 2020-12-16 16:52:53 +0200

slelievre gravatar image

updated 2020-12-16 19:38:15 +0200

Say a graph G has nine vertices numbered 1 to 9 and we want the grid layout in the question.

One easily defines a dictionary of positions.

The set_pos method then lets us assign those positions to the graph.

The positions can also be set when creating the graph, using the pos=... optional argument.

For example, define the vertex set.

sage: V = [1 .. 9]

Then the position dictionary:

sage: pos = {v: (n % 3, -(n // 3)) for n, v in enumerate(V)}

Now build a graph with those vertices, no edges, and those positions:

sage: G = Graph([V, []], format='vertices_and_edges', pos=pos)

Plot it:

sage: G.plot()

Manual grid graph, no edges, set positions

If we start from an adjacency matrix, the vertices will be numbered from 0.

Start from the matrix in the question and remove one of row (chosen so the resulting matrix is symmetric):

sage: A = matrix([[1, 1, 0, 1, 0, 0, 0, 0, 0],
....:         [1, 1, 1, 0, 1, 0, 0, 0, 0],
....:         [0, 1, 1, 0, 0, 1, 0, 0, 0],
....:         [1, 0, 0, 1, 1, 0, 1, 0, 0],
....:         [1, 0, 0, 1, 1, 0, 1, 1, 0],
....:         [0, 1, 0, 1, 1, 1, 0, 1, 0],
....:         [0, 0, 1, 0, 1, 1, 0, 0, 1],
....:         [0, 0, 0, 1, 0, 0, 1, 1, 0],
....:         [0, 0, 0, 0, 1, 0, 1, 1, 1],
....:         [0, 0, 0, 0, 0, 1, 0, 1, 1]])

sage: A.nrows(), A.ncols()
(10, 9)
sage: Arows = A.rows()
sage: del Arows[4]
sage: B = matrix(Arows)
sage: B.is_symmetric()
True

Define positions for vertices 0 to 8 and build a digraph from that matrix with those positions:

sage: pos = {n: (n % 3, -(n // 3)) for n in range(9)}
sage: D = DiGraph(B, format='adjacency_matrix', pos=pos)
sage: D.plot()

Manual grid graph from matrix, set positions

Note that without setting the positions ourselves, the default "spring" layout algorithm would already do a very good job on the grid graph, starting from the corrected matrix.

sage: D = DiGraph(B, format='adjacency_matrix)  # don't set pos
sage: D.plot()

Manual grid graph from matrix, auto layout

The positions have not been set at the time of creating this graph. Defines pos as above, and running

sage: D.set_pos(pos)
sage: D.plot()

gives the same output as when we defined D = DiGraph(..., pos=pos) above.

Sage has a built-in GridGraph constructor which labels the vertices by their coordinates and positions them in a grid all by itself.

sage: G = graphs.GridGraph((3, 3))
sage: G.plot()

Grid graph using GridGraph

This gives an undirected graph.

Turning it into a directed graph is easy:

sage: D = DiGraph(G)

This preserves the positions!

One can also relabel the vertices:

sage: D.relabel([1 .. 9])

This also preserves the positions!

To sum up, the easiest way to achieve the graph in the question might be:

sage: D = DiGraph(graphs.GridGraph((3, 3)), loops=True)
sage: D.relabel([1 .. 9])
sage: D.add_edges((i, i) for i in D.vertices())
sage: D

Regarding the customisation of vertex and edges labels, start by checking the documentation and/or the many questions and answers on Ask Sage which provide instructive examples.

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Asked: 2020-12-16 11:52:25 +0200

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Last updated: Dec 16 '20