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

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15
votes
1answer
679 views

How can I conveniently call igraph through RLink?

Mathematica has lots of functions for working with graphs, but this functionality is not yet as mature as the igraph library. It is useful to have access to igraph from Mathematica, both for ...
5
votes
2answers
214 views

Is there something wrong with VertexConnectivity

As I noticed in the documentation VertexConnectivity is defined as the following The vertex connectivity of a graph $g$ is the smallest number of vertices whose ...
6
votes
1answer
100 views

Vertex displacement/merging in graph?

Given a Graph such as the one produced with the following code ...
9
votes
2answers
900 views

Mathematica Package for Bayesian Networks

Are there any packages that allow the simulation of Bayesian Networks with Mathematica? I found what seemed to be a promising package (Dynamics) on a Brown University URL, ...
17
votes
2answers
1k views

Drawing pairs (planar 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 ...
-5
votes
0answers
49 views

Solve Linear Programm [on hold]

I got the following LP problem and have to solve it. Obviously, the y in the objective function needs to be replaced by constraint 2. These are the current values for H,L,f. Any ideas, how I can ...
0
votes
1answer
34 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 ...
12
votes
2answers
255 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 ...
4
votes
2answers
66 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 ...
15
votes
6answers
441 views

How can I remove B -> A from a list if A -> B is in the list?

I have a list of transformations like this: list = {"A" -> "B", "B" -> "A", "C" -> "D"} As this is used to plot an undirected graph with ...
6
votes
1answer
265 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
40 views

How to plot graphs with vertices positioned as spread as possible? [closed]

The following code, outputs the graph below: graphList = {{1, 2}, {1, 3}, {1, 4}, {2, 5}, {3, 6}, {4, 7}} Graph[UndirectedEdge @@@ graphList] Is there some way ...
-3
votes
0answers
41 views

Interactive model of the PageRank vector! [closed]

You will next build an interactive model in Mathematica for calculating the Page Rank vector of small scale web graphs, with nodes representing websites and edges representing hyperlinks. The number ...
0
votes
2answers
68 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: ...
2
votes
1answer
53 views

Check Specific Connections within Graph

Say you have the skeleton of a graph: nodeset= PolyhedronData["Icosahedron", "SkeletonRules"] and you've an arbitrary list of some fraction of those nodes, say ...
3
votes
1answer
142 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
1answer
31 views

Create vector for each vertex in a network [closed]

I have a network with x vertices and I would like to create a vector with random numbers for each vertex in this network. I would like to generate this list and represent it in a table. Further, it ...
2
votes
1answer
199 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 ...
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 ...
1
vote
1answer
43 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 ...
14
votes
3answers
3k views

How to generate random directed acyclic graphs?

How to programmatically build random directed acyclic graphs (DAG)? I know about the AcyclicGraphQ predicate and the ...
4
votes
1answer
117 views

Why can't I export graphs with loops in V10?

I don't understand why the following does not work: ...
7
votes
1answer
203 views

Finding Rings In A Network

I am doing a research on networks which consist of polygons with different number of sides. I am trying to find all rings (or cycles) in a network. As an example, consider the following graph: ...
2
votes
1answer
65 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 ...
22
votes
3answers
2k views

How to generate a random tree?

Is it possible to generate a random tree without explicitly constructing a random adjacency matrix that satisfies tree properties? How about a random directed tree? Edit: incredible answer by ...
6
votes
3answers
677 views

Random Geometric Graphs

I'm trying to implement an application which uses random geometric graphs in Mathematica, but it seems Mathematica lacks the functionality. I need the following functionalities: Generate a set of ...
16
votes
3answers
1k views

Creating diagrams for category theory

Lately I've been doing algebra and I have found myself drawing a bunch of diagrams when I attempt to solve a problem. Most of the diagrams are very simple so I thought, I bet I can do this in ...
8
votes
1answer
319 views

Caching of Graph Graphics

In this answer, Simon Woods concludes that when you display an expression with head graph more than once, something is getting stored somewhere. I looked into it too and found out this only happens if ...
7
votes
5answers
364 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 ...
3
votes
2answers
126 views

Hasse Diagrams in Mathematica using an arbitrary relation

As a kludge to draw Hasse diagrams for an assignment, I wrote(based on this): ...
0
votes
1answer
49 views

Why Infinity edges with WeightedAdjacencyGraph [closed]

I can't understand why WeightedAdjacencyGraph wants Infinity weight when there are no edges between two nodes. In particular ...
1
vote
1answer
36 views
1
vote
2answers
53 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 ...
4
votes
2answers
146 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", ...
1
vote
1answer
37 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 ...
2
votes
1answer
78 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 ...
22
votes
2answers
3k views

How to play with Facebook data inside Mathematica?

I saw this post from Wolfram here and I would like to know how to import facebook data into Mathematica.
4
votes
3answers
178 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
69 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, ...
6
votes
1answer
139 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 ...
1
vote
2answers
88 views

getting vertices in order from spanning tree

I've got spanning tree for some weighted graph (edges labeled 1-6) - for example: ...
1
vote
1answer
111 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 ...
0
votes
1answer
207 views

Mean path length of randomly generated graphs

I am looking to find the the average path length of 1000 random graphs with the following degree distribution, a few of the vertex degrees are included below ...
1
vote
1answer
60 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 - ...
5
votes
3answers
93 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. ...
1
vote
1answer
93 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)? ...
2
votes
1answer
38 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 ...
4
votes
1answer
129 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 ...
2
votes
2answers
396 views

EdgeRenderingFunction question

Bug introduced in 9.0 and fixed in 10.0.0 (Edit 1 : I added this paragraph after the original post, for context) Some context for this question can be found in another post ...
12
votes
6answers
378 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 ...