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

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2
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1answer
72 views

How to invoke default VertexShapeFunction and EdgeShapeFunction from custom ones?

For this question, g is a Graph object (of order ~2K) such that the VertexWeight and ...
2
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1answer
227 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 ...
2
votes
1answer
158 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
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1answer
145 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 ...
2
votes
1answer
185 views

Arranging “ranked” nodes of a graph symmetrically

I have Markov chains with a pair of absorbing states taken from the $n$-length strings formed from {"H","T"} for n at least 3 ...
2
votes
1answer
63 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 ...
2
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2answers
110 views

Checking connectedness of a graph

I am trying to use the Combinatorica package in a Mathematica version 8 in the following code: ...
2
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1answer
277 views

Finding a Moore neighborhood connected path of bright pixels along the contour of a text character

I have a simple image, for example a blowup of a Times New Roman character like 'R' saved as a PNG. I then perform the following operations to extract a minimum representation of the contour lines ...
2
votes
2answers
525 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 ...
2
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3answers
219 views

Graph with $\{a,b\}$ as Vertex Instead of Number

I'm trying to create a graph which has $\{a,b\}$ as labels: ...
2
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1answer
990 views

Adding an image background to a graph that uses vertexposition

Hello Mathematica stackexchange community! I need your help on a research project. I'm looking to create a graph g with vertices in specifies places and then use an image I have as the background of ...
2
votes
1answer
155 views

What is the best way to save a large graph object, allowing it to be reloaded quickly in a new kernel?

I generated a very large graph, too large to simply display and manipulate with copy/paste operations. How can I somehow save the graph to a file to allow it to be rapidly reloaded after I quit out ...
2
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2answers
183 views

Most efficient way to output a cycle starting from an unordered list of graph vertices

I have some graph $G$ and a list of vertices $(v_1, ..., v_N) \in V$. Using graph structures in Mathematica version 9.0, what is the most efficient way to determine whether or not $(v_1, ..., v_N)$ ...
2
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2answers
491 views

Edges and crossing

I want to make a program where I have a collection of labeled vertices and edges between the vertices such that they join up with edges $a_{1} a_{2}, \; a_{2} a_{3}, \ldots ,\; a_{n} a_{1}$, so the ...
2
votes
1answer
300 views

Speed up iterated manipulations of a graph / table

I am trying to generate a version of Watts' model of cascading shocks to a network following the discussion on p. 20-25 of this article. The basic premise is to use the ...
2
votes
1answer
66 views

How to enlarge a specific part of a graph using Plot Command? [duplicate]

How to enlarge the closed curves of any Graph and Show them in a separate Graph within the ...
2
votes
1answer
59 views

Deleting Isolated subgraph in a graph

Suppose I have a graph GraphPlot[{1 -> 2, 2 -> 1, 3 -> 1, 3 -> 2, 4 -> 1, 4 -> 2, 4 -> 4, 5->6}] Now I want to identify the vertices of a subgraph which are isolated from the main graph.(In this case ...
2
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1answer
63 views

Changing edge weights in a graph using PropertyValue

I encountered a problem trying to change the EdgeWeights in a graph. I am runnning Mathematica 10.1 under Windows 7 Enterprise. I have an undirected graph with 144 nodes and 576 edges. I first ...
2
votes
1answer
58 views

How to draw vertices with identical names multiple times?

I have a list of rules that I would like to show as a layered graph. However, some vertex names appear more than once. How would one best deal with this situation? Example: ...
2
votes
1answer
98 views

Multiple colors on a single graph edge?

Is there any way to put two colors on one single graph edge? For example, I want to highlight two cyclic paths (red and blue). But, if I put the two colorings into one image, it does not work as I ...
2
votes
1answer
70 views

Count graphs with fixed number of vertices incluing isomorphisms [closed]

I'm trying to use the listgraph function in the Combinatorica package: Needs["Combinatorica`"] g = ListGraphs[5]; ShowGraph /@ g However, it only returns all the ...
2
votes
1answer
177 views

Community detection on weighted graphs?

The documentation says that FindGraphCommunities works with weighted graphs. I've been playing around with a complete graph with weighted edges, and FindGraphCommunities always returns a single ...
2
votes
1answer
187 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
252 views

Want to label vertices of a graph and manually move them around

I would like to plot a graph in such a way that The vertices are labeled using labels that I've given them, rather than just their number, I can manually move the vertices around. In the code ...
2
votes
1answer
66 views

Reversibly abstracting a list of strings as a graph object where vertices represent strings and edge connect pairs of strings based on various tests

Imagine I provide you a list of arbitrary strings, say: Map[StringJoin, Tuples[{"0", "1", "2"}, 4]]. I'd like to abstract these strings as a graph object in ...
2
votes
1answer
688 views

Create a graph from KML file

I'm wondering how I can take a .KML (Keyhole Markup Language) file and convert/express it as a graph for use in Mathematica. Even just in general, is it possible to convert a KML file to a graph? I'm ...
2
votes
1answer
438 views

GraphPath: *all* shortest paths for 2 vertices, edge lengths negative

Mathematica uses Bellman-Ford to find a shortest path between two vertices when the edge lengths are negative: ...
2
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1answer
109 views

PermuteSubgraph not working? (Combinatorica)

I am trying to write a code to perform the QAP partialling analysis (here's a paper to know more) but the part in which I "scramble" the graph with PermuteSubgraph does nothing, I am actually not ...
2
votes
1answer
141 views

Is it possible for me to explicitly specify a point list for SpatialGraphDistribution?

The function RandomGraph[SpatialGraphDistribution[n, r]] generates a random geometric graph over $[0,1]^2$ where vertices are connected if they are within a ...
2
votes
1answer
159 views

VertexList ordering of a simple graph

Given a simple graph like g=Graph[{b -> c, a -> b}] I would like to have f[g] resulting in ...
2
votes
1answer
339 views

Changing some stuff to Kruskal's Algorithm

I'm trying to modify this algorithm: http://demonstrations.wolfram.com/ConnectingTownsUsingKruskalsAlgorithm/ The thing is that I want to receive a Graph (declared outside, with all its vertex, edges ...
2
votes
0answers
48 views

How to understand the LocalClusteringCoefficient use in directed graph? [duplicate]

When this function use in undirected graphs,its action is normally and can be explained by this formula $$CC_v=\frac{n}{C_{k}^{2}}=\frac{2n}{k(k-1)}$$ n is adjacent nodes of $v$'s number of ...
2
votes
0answers
114 views

How to make a flowchart? [closed]

I'd like to make a flow chart in similar to this: I think it's more of a layout and stylistic question for a graph - how to style a graph with labeled edges and vertices so that it looks like a ...
2
votes
0answers
81 views

How do I get all possible paths in terms of edges, and not vertices in Mathematica?

Suppose I have an undirected graph ...
2
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0answers
37 views

Algorithm to determine if two colored graphs are isomorphic? [duplicate]

I have two (vertex-)colored graphs. I want to determine if they are isomorphic, with the condition that the isomorphism respects the colors of the vertices. Moreover, I want the algorithm to output ...
2
votes
0answers
92 views

Graph, overlapping vertexlabels

The graph I create is based on more then 1000 different word-combinations. A example looks like this: text = {{word, word1}, {word1, word2}, {word1, word3}, {word,word4}, {word,word5}, ...
2
votes
0answers
50 views

Custom graph distribution

I am working with random graphs a lot. It's quite easy to describe random graph using, adjacency matrix or just a list of edges. However I am thinking that I might benefit from describing random ...
2
votes
1answer
283 views

Distinguishing left from right adjacent triangles in triangle mesh [closed]

What I'm trying to do: I'm trying to create a path-drawing function which will produce a path like the one I-P in the diagram below. The way this path was generated requires me to swap between the ...
2
votes
0answers
59 views

Bugs in VertexContract function?

I think there may be two bugs in the VertexContract function: 1) The updated graph does not include reasonable edgeweights 2) The function does not actually reduce the number of vertices in the ...
2
votes
1answer
49 views

VertexConnectivity and FindVertexCut disagree [duplicate]

I'm trying to use Mathematica to compute the minimal vertex cut for graphs. From what I understood, VertexConnectivity of a graph should correspond to the number of vertices in the minimal vertex cut. ...
2
votes
0answers
96 views

Is there a minor bug in Neal Alexander's TopologicalSortAll[]?

There is an amazing answer to this question: All possible topological orderings of a graph By Neal Alexander. However, as user "dark blue" (I am not this user) notes: ...
2
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0answers
74 views

Choosing a List as VertexWeight for a TreeGraph

I would like to map every vertex of my TreeGraph to an List. ...
2
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0answers
103 views

Belief Network, Bayesian network

There is already a question about simulating Bayesian networks with Mathematica (Mathematica Package for Bayesian Networks). However, are there any packages or approaches which help in computing the ...
2
votes
1answer
392 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 ...
2
votes
0answers
77 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 ...
2
votes
0answers
86 views

Get correlation matrix when using FindGraphCommunities

Does somebody know how to get the correlation matrix when using FindGraphCommunities (Social Network analysis) using the "Spectra" option? Can somebody tell me as ...
2
votes
0answers
58 views

How to use Automorphisms[] on a graph? [duplicate]

I am having difficulty mixing the new post-Combinatorica graph data structure, with functionality apparently only in Combinatorica. I have constructed a graph using ...
2
votes
0answers
329 views

Why my Mathematica 9.0.1 wont work with some samples of Mathematica in Graph Theory?

Bug introduced in 9.0 and fixed in 10.0 FindMinimumCostFlow is introduced in 9.0. I updated my Mathematica recently to 9.0.1 cause the previous version was ...
2
votes
0answers
229 views

Fast calculation of commute distances on large graphs (i.e. fast computation of the pseudo-inverse of a large Laplacian / Kirchhoff matrix)

I have a large, locally connected and undirected graph $G$ with $\approx 10^4$ vertices and $\approx 10^5$ to $\approx 10^6$ edges. Moreover I can bound the maximum vertex degree as $Q_{max}$. I ...
2
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0answers
120 views

Strange double evaluation using MorphologicalGraph

(MMA 9.0.0 on Mac OS/X 10.8) Please consider the following snippet (this is as SMALL as I could make it -- my attempts at making a smaller repro-case eliminated the effect that I am investigating) ...