Questions about handling graphs in Mathematica, graph theory, graph visualization, GraphPlot, the built-in Graph type and the Combinatorica` package.

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3
votes
0answers
100 views

Undirected Network and its Monte Carlo Simulation

So I have this array of points, in the form {x, {y,z}}, where x is the node number assigned when I used the locator pane to make a network, and y and z are its unitary coordinates. The graph is made ...
4
votes
1answer
105 views

Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
2
votes
1answer
91 views

Cellular Automata Neighborhood as Node connections

Can I use the CellularAutomation[] function where the neighborhood is defined by the connections between nodes? For example, if 1 -> 2, 1 -> 3, 1 -> 8, 1 ->1, then the neighborhood of node 1 is the ...
3
votes
0answers
37 views

Does anyone know the options for “HierarchicalEdgeBundling” in Mathematica?

I'm looking to reproduce the types of graph layout that are possible in D3 (http://bl.ocks.org/mbostock/7607999) in Mathematica. Since Mathematica doesn't explicitly support force directed edge ...
3
votes
2answers
105 views

Harmonious graph labeling

Is it possible to harmoniously label a graph in Mathematica? I would like a function, that when given a graph, would return a harmonious labeling. If not, is there other software that can do it? A ...
2
votes
4answers
89 views

How to plot a graph from it's incidence matrix?

I'm using Mathematica v9 and am trying to draw a graph by using it's incidence graph, but it won't draw it, which occurs an error "is not a valid incidence matrix.". But I've checked my matrix, and ...
6
votes
2answers
255 views

How to color edges of a graph which has multiple edges connecting certain vertices

I'm studying BIBD(Balanced Incomplete Block Design) and want to draw some graphs by coloring their blocks in different colors, respectively. A block is a collection of edges (or vertices). For ...
2
votes
1answer
40 views

Hungarian Algorithm using BipartiteMatchingAndCover Function

I have a bipartite graph with two sets of vertices. ...
4
votes
1answer
80 views
2
votes
2answers
216 views

Manipulate graphs in 3D

Is it possible to Manipulate Graphs (e.g. a ...
18
votes
5answers
893 views

How can I replace bi-directional DirectedEdge pairs in a Graph with a single UndirectedEdge?

The Cayley graphs produced by Mathematica 8.0's CayleyGraph function represent actions that are their own inverses in an unconventional way: rather than using a ...
10
votes
4answers
8k views

Finding all simple paths between two vertices in a graph

There are built-in methods to find a shortest path between two vertices in a graph, and the question on finding all shortest paths between two vertices has gathered quite a bit of attention. A path ...
2
votes
3answers
212 views

How to draw a combinatorial graph with different colors of edges?

For example, like above. I've read some examples and descriptions in here, but couldn't figured it out.
3
votes
1answer
45 views

Make AdjacencyGraph hide single unconnected elements

Is there a way to force AdjacencyGraph to hide single unconnected or self connected elements? ...
8
votes
1answer
160 views

Dual graph of an arbitrary (planar) graph

Every planar graph has a dual. How can I obtain it with Mathematica? I know that GraphData provides the DualGraph property for ...
13
votes
2answers
547 views

Animating transition between all graph representations obtained from curated data

Pappus graph is one of many graphs whose various data is contained within Mathematica. Mathematica typically keeps several ways of representing such graphs: ...
5
votes
3answers
153 views

Converting expressions to “edges” for use in TreePlot, Graph

This question is similar to this: Nested list to graph. How to "flatten" an arbitrary expression, eg expr = a[b[c, d[e][f], g], h] to a list of key-value pairs ...
0
votes
1answer
80 views

Generate Random 3D Network using GraphPlot3D and loop

Instead of writing all this out I want to do the same thing with a loop and be able to manipulate n and k. The idea is to create a randomly generated network where n is the number of nodes and k is ...
14
votes
2answers
765 views

Drawing pairs (graph, circle packing)

Circle packing theorem states: For every connected simple planar graph G there is a circle packing in the plane whose intersection graph is (isomorphic to) G. How to use Mathematica to draw examples ...
0
votes
1answer
159 views

Creating a Network from a Output

So I used the locator pane to derive the positions of a vertex on a picture. The picture was the Maryland Power Grid and the vertices were the generators and loads of the power system. When I clicked ...
1
vote
2answers
79 views

How can I speed up the export of graphs in DIMACS format?

I'm creating random graphs with suitable properties and exporting them in the DIMACS format. Already, for rather small graphs with, say, ~60k vertices and ~240k edges, ...
14
votes
4answers
455 views

Can TreeForm be displayed “sideways”?

One recurrent problem I'm having with displays generated with TreeForm is that the expressions to be so displayed often at least one level with many (> 20) nodes ...
2
votes
3answers
242 views

How to find a path that traverses each edge of a graph exactly twice?

I have a question regarding a graph traversal problem. This is the graph I am working with: ...
28
votes
8answers
1k views

Longest path in 0/1 matrix

I have a matrix of 0's and 1's forming a number of disjoint paths:   I would like to find the lengths of the paths, and from that "spectrum," the longest length (in the above example: 27, ...
4
votes
2answers
99 views

How to obtain all the distinct De Bruijn sequences?

In combinatorial mathematics, a $k$-ary De Bruijn sequence $B(k, n)$ of order $n$ is a cyclic sequence of a given alphabet $A$ with size $k$ for which every possible subsequence of length $n$ in $A$ ...
6
votes
2answers
118 views

Why the Mouse dragging response not as smooth as Locator

I am experimenting to use MouseDragged eventhandler to change the vertices positions of a triangle, it works, but not as smooth as using Locators. Is this the ...
1
vote
0answers
171 views

Map of all graphs obtainable with GraphData?

I've been trying to put together an answer to another question, but I am stuck, so I decided to post this question instead. Mathematica contains (among its curated data) information on definition, ...
5
votes
3answers
221 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
4
votes
1answer
103 views

The algorithm of ListGraphs[n,m]

I'm not sure if this is a Mathematica problem, math problem or a CS problem, so if this is off-topic please transfer it. In the package Combinatorica there is a ...
3
votes
2answers
98 views

Vertex Names of Subgraph in Order of Connectivity

I extract path subgraphs $P_4$ of an undirected graph $G$. And want to list the VertexNames of the subgraphs in the same order as they are connected. Here is an example: ...
1
vote
1answer
118 views

How to generate a random binary tree with a given number of vertices and with a given shape, namely compact or elongated

I tried to generate a random binary tree with a Table of RandomInteger and to give a shape with a ...
0
votes
0answers
31 views

Find set of subgraphs of g1 isomorphic to g2 [duplicate]

I would like to find all the subgraphs of a given graph g that are isomorphic to the graph h. My current code doesn't work how it should. Many solutions are missed and I think something is ...
2
votes
3answers
140 views

Sequence of binary trees with different source nodes and with the same Strahler hierarchical order

I would like to create a picture which contains a sequence of binary trees with the same Strahler hierarchical order (for example equal to 2) e with a sequence of different source nodes "i" (from 1 to ...
0
votes
0answers
33 views

how to rewire the minimum number of edges in a disconnected bipartite graph, so to transform it in a connected one

Consider an incidence matrix A for a bipartite graph (Aij=1 if node i of group 1 and node j of group 2 are connected). A is not symmetric. Assume that A is disconnected or only weakly connected, i.e. ...
6
votes
4answers
2k views

How to generate and draw simple bipartite graphs?

A bipartite graph is a graph whose vertices can be divided into two disjoint sets. Given two lists: {1, 2, 3} and {x, y, z}, ...
1
vote
1answer
71 views

Rendering of a HighlightGraph in a Manipulate content pane distorted by changing the highlighted edge

A HighlightGraph inside a Manipulate initially displays correct however after approximately 2 seconds, the layout changes and ...
3
votes
2answers
89 views

Labeling vertices by number in Graph: Getting text to display at the right size

Minor aesthetic question here. I was playing around with Graph's and decided to render a cute-looking family of directed graphs, with the vertices being the number ...
3
votes
0answers
129 views

Understanding performance: graph connected components

I need to analyze directed graphs with 10M edges, 1M vertices, and 300K strongly connected components, so that the largest one contains 400K vertices. I read some explanations of Leonid Shifrin here, ...
1
vote
2answers
68 views

Using Combinatorica`ListNecklaces in v9

I am using Mathematica for visualization of DeBruijn graphs. However, I am having a bit of trouble using ListNecklaces. I want to know how many cyclic shifts of ...
2
votes
1answer
119 views

distance between each vertex of a graph and its output

I have a question regarding this Q&A. Let's call a vertex that is not the tail of any directed edge an output of the graph. The graph below has only one output (at the far right). If I want the ...
13
votes
5answers
437 views

Graph from binary matrix (not adjacency) respecting the original matrix positions

I have a binary matrix. My objective is to connect every close (without "jump") elements with value equal to 1, but I must keep the point positions, just like it's shown at the image. Can somebody ...
0
votes
0answers
62 views

Centrality measures and normalisation

Are centrality measures normalised in Mathematica 9? Only ClosenessCentrality is normalised. How I can normalise other centrality measures notably ...
8
votes
2answers
271 views

Graphing a network with state transition flows (of varying size)

In one of Stephen Wolfram's recent blog posts (http://blog.stephenwolfram.com/2013/04/data-science-of-the-facebook-world/#more-5350) he provides the network plot below. The size of the arrows that ...
1
vote
0answers
99 views

Triangular lattice with periodic boundary conditions

I am trying to generate an equilateral triangular lattice with fixed vertices and periodic boundary conditions. I am supposed to assign an index (starting from 0) to each vertex in my lattice and then ...
1
vote
0answers
51 views
1
vote
2answers
144 views

Error changing edge thickness in a GraphPlot

I'm having some problems with the Mathematica graphics inspector. I want to make a graph with the following code: ...
8
votes
3answers
405 views

TreePlot with centered vertexes

I want to draw a tree plot for Euler totient function for this question like the following: I generate the EulerPhi for first 20 numbers into a list: ...
3
votes
1answer
140 views

find cycle in directed graph

Given a digraph G in the form of a list of edges, is there implemented some command that returns a directed cycle in G of ...