Tagged Questions

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

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14
votes
3answers
508 views

How can I construct and visualize a hypergraph?

A hypergraph is a generalization of a graph, in which an edge can connect more than two vertices. Thus you can think of an edge in an hypergraph as a subset of nodes. Since version 8, Mathematica has ...
5
votes
3answers
515 views

Graph and Markov Chain

I have the following code: proc = DiscreteMarkovProcess[1, {{0.6, 0.4}, {0.3, 0.7}}] Graph[{"A", "E"}, proc, GraphStyle -> "DiagramBlue"] How can I 'force' ...
6
votes
1answer
129 views

Replacing graph nodes with matrices

I would like to label a graph with matrices. Suppose the graph is simple: And I have an array mats that contains the labels for vertices 1,2,3,4 (these are just random 0-1 matrices; ignore the ...
0
votes
1answer
84 views

Turning sound into a graph

I'm writing a comprehensive text on graphs and Mathematica and in this context I have this, let's call it, creative gap between sound and graphs. There are plenty of ways one can create graphs from ...
2
votes
1answer
163 views

How to convert a sparsearray to a graph?

s = Import["hello.mat"]; t = GraphEmbedding[Graph[s[[1]]], "GridEmbedding"]; I get the following error: GraphEmbedding::graph: A graph object is expected ...
3
votes
5answers
232 views

Ordering the Boundary points of a Polygon

I feel like this should be simple, but I keep running into walls. Say someone gives you the coordinates of the vertices of a pentagon and the center point of the hexagon. Is there any way to get an ...
3
votes
2answers
257 views

How to create a 'shortest-path link matrix'?

I am currently struggling with a problem in Mathematica. I have a randomly generated weighted Barabasi-Albert graph and a corresponding demand matrix of the same size. I'm generating the graph with ...
3
votes
0answers
86 views

Citation of the algorithms used in FindGraphCommunities [closed]

For my research work I need to put a comparison of different community detection algorithms. Instead of implementing all those algorithms once again, I would like to use the methods already provided ...
4
votes
2answers
217 views

Coordinate extraction and manipulating graphs as graphics objects

Consider the image below: GraphData[{"Wheel", 7}] Is it possible in Mathematica to lay several of these Graph along each ...
1
vote
1answer
49 views

Importing additional custom data in DIMACS format

I have graphs in DIMACS format, with vertex colors specified. The vertex colors are denoted by lines n u c, where u is the ...
8
votes
3answers
434 views

How can one draw a network with nodes and links in a grid shape?

I'd like to be able to use MMa's graphics to make something like this which I know must absolutely be possible (and probably easy) with MMa. I don't actually even need different colors (though ...
1
vote
1answer
51 views

Using FindGraphCommunities, write community membership for each vertex to CSV

I have a network that I've loaded into Mathematica, and I've used FindGraphCommunitites[network,Method->"Hierarchical"] to identify the communities in the ...
1
vote
1answer
87 views
3
votes
1answer
101 views

Expected graph distance in random graph

I am trying to use the functionality of Expectation and Probability for random graphs, in particular for percolation models. ...
3
votes
2answers
137 views

Positioning Vertices in a Graph

I made a graph that has a given number at each vertex: I want to place vertex 1 above vertex 2 if value of vertex 1 is larger than of vertex 2. And also, vertices with same value should be located ...
2
votes
1answer
58 views

Fix the size of vertices and arrow in graphs

I defined an option to draw nicely the graph. But I have a problem with the different size obtained. For example, the layout of the first graph is what I want to have for all other graphs I will ...
3
votes
2answers
90 views

How to get all leaves from a graph's specific node

Let's say I have this graph (The code to generate the graph is at the end) How can I extract all the leaves comming from, let's say "cluster3"?, i.e. {100, 92, 87, 89} I guess I have to first ...
0
votes
0answers
45 views

Graph plotting: specify layers for layered drawing

Mathematica can do layered graph drawing with LayeredGraphPlot or GraphLayout -> "LayeredEmbedding". Is it possible to ...
8
votes
2answers
336 views

Mathematica 10 Graph issue

Please try to evaluate this code in Mathematica 10. ...
3
votes
0answers
130 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
122 views

Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
3
votes
1answer
125 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
43 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 ...
2
votes
4answers
134 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 ...
3
votes
2answers
124 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 ...
3
votes
1answer
61 views

Hungarian Algorithm using BipartiteMatchingAndCover Function

I have a bipartite graph with two sets of vertices. ...
4
votes
1answer
98 views

How to construct a polyhedron from its vertex graph?

Consider the graph given by ...
6
votes
2answers
277 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
3answers
260 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
48 views

Make AdjacencyGraph hide single unconnected elements

Is there a way to force AdjacencyGraph to hide single unconnected or self connected elements? ...
9
votes
1answer
195 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 ...
0
votes
1answer
108 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 ...
0
votes
1answer
169 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 ...
5
votes
3answers
173 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 ...
2
votes
3answers
299 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: ...
1
vote
2answers
84 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, ...
4
votes
2answers
108 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
129 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 ...
4
votes
1answer
108 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
115 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: ...
30
votes
8answers
2k 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, ...
1
vote
0answers
199 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, ...
0
votes
0answers
33 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 ...
3
votes
1answer
144 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 ...
2
votes
3answers
154 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
47 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. ...
1
vote
1answer
82 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
114 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 ...
1
vote
2answers
72 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 ...
3
votes
0answers
154 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, ...