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

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8
votes
1answer
227 views

Vertex merging in graph?

Given a Graph such as the one produced with the following code ...
0
votes
1answer
58 views

Verticepair - route matrix

I have the following problem. I have two lists: list1 defines all possible commodities in a network g. E.g. Form vertex 1 to ...
4
votes
2answers
119 views

Equivalent of RadialOutside for Graph VertexLabels

I'm creating a circular graph and want the labels to be placed on the outside of the vertices in a circular manner on the outside of the graph. I've been playing around with the ...
14
votes
2answers
534 views

How to build a 3D graph from a 3D matrix?

Following this and that question and the corresponding answers, Mathematica can build 2D graph from 2D matrices. Question How to make the corresponding 3D graphs from 3D cubes? Attempt ...
0
votes
2answers
74 views

Getting FerrersDiagram to work

I am trying to generate FerrersDiagram (see http://reference.wolfram.com/language/Combinatorica/ref/FerrersDiagram.html), any clues to getting it to work? I get error message for the following: ...
6
votes
1answer
363 views

Connect neighbouring points as list of segments in 2 D

Context I am interested in connecting neighboring points in 2/3D as list of segments. I am guessing this is something within the reach of graph theory, which is well implemented in mathematica. ...
1
vote
1answer
48 views

Unexpected behaviour with GraphIntersection and GraphDifference

I run into some unexpected behaviour of GraphIntersection and GraphDifference. Behaviour is the same for both so the example is only on the GraphIntersection: Suppose I have two lists of directed ...
9
votes
2answers
252 views

Self-loops in Graph may not display correctly or export correctly to PDF (due to BezierCurve problem)

Bug introduced in 10.0 and persisting through 10.3 Problem is due to a BezierCurve bug. I don't understand why the following does not work: ...
4
votes
1answer
172 views

Vertex Labelling and Word wrap

I am having trouble formatting vertex labels, explicitly adding line breaks to Vertex labels for word wrapping and other purposes. I have explored the pane option suggested here but when I include ...
2
votes
1answer
385 views

Dynamic graph construction and visualization (Watts' “Small Worlds” α-model)

I need some help in creating a Mathematica program for building and visualizing Watts' "Small Worlds" α-model. This is a variant of the more known (and much more simple) β-model (also known as ...
8
votes
5answers
437 views

Is there a neat way to generate the odd set constraints matrix?

Given a undirected graph $G=(V,E)$, I am trying to generate a related matrix $M$, where columns are indexed by $E(G)$ and rows are indexed by all odd subsets of $V(G)$. I can finish this task using ...
1
vote
2answers
99 views

Add weighted edge to a graph in Mathematica 8

Is it possible to add an edge with a specific weight to a Mathematica Graph object? The function EdgeAdd has no option for the weights, nor the ...
1
vote
1answer
53 views

Graph objects for LineGraph

When I enter for example G = Part[GraphData[10],1]; LG = LineGraph[G]; I get error message that LineGraph requires a graph ...
4
votes
2answers
379 views

Hasse Diagrams in Mathematica using an arbitrary relation

As a kludge to draw Hasse diagrams for an assignment, I wrote(based on this): ...
6
votes
3answers
344 views

Enumerating all connected graphs with 9 vertices

The version of my Mathematica is 10. I generate a connected graph with 9 vertices, but find that it is not included in Mathematica. ...
0
votes
0answers
81 views

Mathematically Eliminated in Baseball

Earlier today the Yankees were mathematically eliminated from the playoffs. Determining when this condition is satisfied for any given team is complicated but can be solved as a maximum flow problem, ...
3
votes
1answer
103 views

how to depict a network with a legend

Because my network nodes have real world names more than a few characters long, I'd like to label them with a shortcut, e.g., n1, n2, n3, ..., and put a legend on the side something like this: n1 - ...
2
votes
2answers
178 views

getting vertices in order from spanning tree

I've got spanning tree for some weighted graph (edges labeled 1-6) - for example: ...
2
votes
1answer
336 views

Finding Hamiltonian path in Graph

I have weighted, undirected full graph (generated from points in R^2), where weight between every two vertices are euclidean distance between corresponding pair of points. What I'm trying to do is ...
7
votes
1answer
254 views

Fractal dimension of a large networked molecular system

I am trying to determine the fractal dimension of this complex biomolecule (figure attached). Any clues as to how this can be done. In trying to determine this quantity, I wonder how its ...
2
votes
1answer
171 views

Planar graph layout

Mathematica supplies planar graph layout, which draws a nice picture of a planar graph, but is there any way to get one's hands on the layout? For example, to find its faces (complementary regions)? ...
5
votes
3answers
105 views

GraphIntersection Problem

I Have a problem when plotting 2 functions. I want to find out where the two graphs intersect eachother. That said, I want the coordinates (x, y) of the point. ...
2
votes
1answer
184 views

Dynamic process on graph

I have a question, which I failed to find an answer to myself. I'm a casual user of Mathematica, but do have some knowledge about Dynamic module and other "Advanced" features. My problem is ...
2
votes
1answer
81 views

Mathematica 8: EdgeList and CommunityStructureAssignment shadowing problem

I'm facing some issues when trying to use the CommunityStructureAssignment function from the GraphUtilities package in Mathematica 8. I'd like to output a ...
5
votes
2answers
199 views

Graph expansion on Mathematica

Is there a way by which Mathematica can be given a graph as an input and be asked to find its expansion? Note: By "expansion" I mean the quantity called "isoperimetric number" or "Cheeger constant", ...
9
votes
4answers
306 views

Multiple Forms of Transportation Between Cities

I want to be able to show different connections between cities based on modes of transportation. For instance, you could walk to any city, but it would take a long time, you could take a train, but ...
14
votes
6answers
911 views

Finding all paths of certain length between vertices in path graph, non-simple ones too

First I will tell you what my ultimate goal is, because maybe there's another way of doing it other than what I am trying. I need a list of all $(a_1, a_2, \ldots, a_N)$ tuples that satisfy certain ...
2
votes
1answer
214 views

Creating an Adjacency Matrix to connect an undirected network

I used the locator pane to map a network, specifically the Maryland Power Grid. What I would like is to have some sort of numbering of the vertices on the unconnected network, how to make an adjacency ...
0
votes
0answers
41 views

Graph embedding and edge weights [duplicate]

Does functions like GraphPlot take in to account edge weights in case of springelectrical embedding? In case of spring electrical embedding I expect the vertices connected by heavy edges to be pulled ...
13
votes
3answers
590 views

Binary decision diagrams (BDD)

I would like to use Mathematica to help me simplify a given Binary Decision Diagram (i.e. pick the optimal variable ordering). I don't seem to find anything at all on the topic, although it is ...
6
votes
2answers
133 views

How to use DegreeGraphDistribution with directed graphs?

DegreeGraphDistribution supports directed graphs because it has a DirectedEdges option. How can I specify the in-degree ...
4
votes
1answer
153 views

Undocumented overload for Graph?

I stumbled (here, in the expression for the block diagram) upon a version of Graph that I don't see in the documentation over here. That documentation admits three overloads (the following are in my ...
5
votes
0answers
265 views

How to draw block diagrams as Graph objects?

In the documentation ClosedLoopResponsesWithAPIDController, There is a very nice block diagram. I want to create my own block diagrams similar to this. I clicked on the diagram and pressed ...
8
votes
1answer
448 views

Coloring edges of a graph according to their weight?

What's the simplest way to plot a graph with weighted edges, such that the color of the edge corresponds to the weight of the edge?
18
votes
3answers
1k 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
929 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' ...
7
votes
1answer
163 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
217 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 ...
3
votes
1answer
373 views

How to convert a sparse array 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 ...
4
votes
5answers
874 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
419 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 ...
6
votes
1answer
308 views

Citation of the algorithms used in FindGraphCommunities

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
274 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
68 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
677 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
114 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 ...
4
votes
1answer
137 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. ...
5
votes
2answers
579 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
155 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 ...
2
votes
0answers
76 views

What Algorithm Does Mathematica use to Calculate Betweenness Centrality for Unweighted Graphs?

I recently asked this question on the Mathematics SE. Does anyone know, as a follow up, what algorithm Mathematica uses to calculate the betweenness centrality vector (of $N$ elements) for an ...