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

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1
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1answer
144 views

Community structure algorithm [closed]

I'm using CommunityStructureAssginment[] from GraphUtilities but not sure what is the algorithm behind it. May be someone knows what is the algorithm? Or any info on the community structure ...
6
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1answer
504 views

How to turn a random graph into a matrix

I have constructed a random graph with Mathematica using the RandomGraph command. Now I would like to convert this graph to a matrix, but I don't know how. The ...
7
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3answers
236 views

How can I efficiently check if a graph is unit distance?

A unit distance graph is a graph that is embeddable in the plane so that every edge has length 1. ...
3
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2answers
278 views

Combinatorica: Girth[] and FindCycle[] disagreement

Warning: run the following code in a fresh Mma session, as some symbols could be shadowed (depending on your Mma version) While trying to answer this question, I fell into the following: ...
4
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2answers
203 views

Odd behavior of GridGraph and DirectedEdges

For some reason the option DirectedEdges->True, albeit working internally with grid graph, does not appear in the visualisation for 1D and 2D graphs. It also ...
2
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1answer
119 views

Using EdgeList on a once empty Graph crashes the kernel

Note: this is fixed in version 9. Calling EdgeList on a non-empty graph which was previously empty causes the math kernel to crash. For example, ...
12
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4answers
1k views

Finding elementary cycles of (directed) graphs

I need to enumerate all the simple cycles (i.e. elementary cycles where no vertex is repeated other than the starting) of a graph which has both directed and undirected edges, where we can treat the ...
4
votes
1answer
169 views

Enhancing GraphUtilities' GraphEdit

One thing I use Mathematica for is building molecular graphs. Until now, I've been content with generating an adjacency matrix from SMILES data, and passing that to ...
10
votes
2answers
419 views

Proper way to add vertices to an adjacency matrix

I'm looking for a robust way to add vertices to a graph by modifying its AdjacencyMatrix. Here's what I have so far: ...
5
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3answers
169 views

StandardForm on Graph edges

The Graph command displays edge labels in TraditionalForm. I instead want to use ...
12
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2answers
1k views

How to convert an image to a graph and get the positions of the edges?

I am trying to convert an image to a graph. My image is already skeletonized and looks pretty much like this: What I need to do is identify all vertices and edges, and in particular get a list of ...
7
votes
4answers
305 views

Can I stop edges in graphs from drawing on top of the vertices?

Consider the following testadj = RandomVariate[BernoulliDistribution[0.15], {50, 50}]; AdjacencyGraph[testadj, VertexSize -> Large] The nodes are almost ...
14
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3answers
995 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 ...
16
votes
3answers
429 views

How to get complete Documentation Center graph of guide pages?

On the very last image below you can see a typical path of walking through Documentation Center guide pages. What is the best way to get the graph data and visualize the whole structure of these ...
2
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1answer
144 views

GraphEdit making edges straight

When using a GraphEdit to alter a graph, is there a way to make the edges straight from one vertex to another? Thanks Here is my code: ...
1
vote
1answer
189 views

Recovering vertex names from Combinatorica Graph

According to WRI tech support: Combinatorica functionality is not technically deprecated, though it is our hope that future versions of Mathematica will subsume it entirely by incorporating its ...
2
votes
2answers
192 views

Working around behaviour of EdgeRenderingFunction

One can make graphs GraphPlot[{1 -> 2, 2 -> 3, 3 -> 4, 4 -> 5, 5 -> 1, 1 -> 1, 5 -> 5}] and one can generalize the input such that one ...
3
votes
2answers
105 views

Turning evaluation off

I am making a directed graph, but Mathematica keeps trying to evaluate my labels. I know that I can just use " ", but I have a lot of input. Is there a way to turn evaluation off? ...
7
votes
2answers
771 views

Is it possible to export a graph as graphic to Excel?

It is straightforward to export lists to Excel with Export. Can I export a graphic image, too? This does not work: ...
4
votes
1answer
210 views

Counting the size of the minimum cut produced by MinCut of GraphUtilities`

I want to use the MinCut function of the GraphUtilities` package to find minimum cuts for a few graphs. I'm completely new to ...
5
votes
1answer
934 views

When do I use Mathematica, when do I use Gephi, and how do I use them together?

Mathematica has great operations for analyzing graphs but when the graphs are a bit bigger, Gephi seems to be more efficient (at least on my computer) at drawing and analyzing, i.e. visualizing the ...
6
votes
3answers
552 views

Graph adjacency matrix with unconnected nodes

I am trying to display a series of 9x9 adjacency matrices which represent directed graphs on a 3x3 grid. The issue I am running up against is this (compounded by that fact that I don't really know how ...
21
votes
1answer
1k views

Is there a way to convert an image into a Graph?

I'm trying to convert an image with several overlapping dots into a Graph. The goal is to be able to derive the Kirchhoff matrix for the randomly created "network ...
2
votes
2answers
148 views

Is it possible to use PropertyValue to modify properties of Graph objects in a list?

This post can be seen as a follow up to Property assignment on a graph vertex using PropertyValue does not work inside a function. I have defined a function: ...
3
votes
1answer
180 views

Bring Vertices to the foreground

I'm having some issues with being able to trigger the Tooltip in an AdjacencyGraph, as the edges are "covering" the vertex labels. In the example provided, there are no issues to display the tooltip ...
2
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0answers
195 views

How to predict some constant number of values with NeuralNetworks

Example: << NeuralNetworks` data = {Sin[#]} & /@ Range[0, 4 Pi, 0.5]; learn = data[[1 ;; 15]]; Now, lets fit our neural network: ...
13
votes
2answers
933 views

Creating a graph with variable size of vertices and variable thickness of edges

I'm trying to create a graph to represent transitions between different states of a system. I would like to represent the time the systems spent in a state with the size of the vertex and the ...
20
votes
1answer
810 views

Graph vs GraphPlot

What is the difference (in purpose) between Graph and GraphPlot? Which function is bested suited to which tasks? Background: I ...
7
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2answers
548 views

Controlling TreePlot (and GraphPlot) layout issue

A continuing battle with Mathematica involves graphics heavy with text labels. For example, the following expression renders so that the "Lifecycle properties..." ...
6
votes
2answers
231 views

How do I reorder vertices in a graph?

I have a directed acyclic graph $g$, and I'd like to re-order the vertices in this graph object such that when I call VertexList[myGraph] the vertices appear in ...
10
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1answer
183 views

Issue with PathGraph

I am having a strange issue with PathGraph. Executing PathGraph[{a, b, c}] or ...
5
votes
0answers
253 views

How to compute the genus of a Graph? [closed]

What's the simplest way to compute the genus of a graph using Mathematica? I have looked for a Genus function (even in the ...
6
votes
1answer
140 views

Vertices, their labels, and how to refer to them?

In the examples I have seen, graph vertices in Mathematica are usually explicit small integers. However, Wolfram documentation says that vertices can be any arbitrary expression (eg., george, x^2, ...
18
votes
5answers
889 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
2answers
420 views

Select a directed SubGraph without sinks and sources

Consider the following problem: Assume you have a large list of directed edges, that constitute a large graph. I would like to provide an initial subset of vertices and I need to know which additional ...
11
votes
1answer
310 views

Ulam's Spiral with Opperman's diagonals (quarter-squares)

First we craft a function to return the quadrant boundary based on Oppermann's Conjecture a[n_] := (Mod[n, 2] + n^2 + 2 n)/4 Then we create a few lists ...
5
votes
3answers
282 views

Rendering polygon as graph with directed edges in Mathematica

In Mathematica I'm trying to render a polygon as a set of vertices and directed edges. What I have so far: ...
8
votes
2answers
289 views

How do I convert this Nicomachus's Triangle to one with edges?

I want to put edges on this Nicomachus's Triangle r = 7; t = Table[2^(n - k) 3^k, {n, 0, r}, {k, 0, n}]; ColumnForm[t, Center] Is there an easy way to do this? ...
10
votes
2answers
270 views

Using Gather to rearrange my data

I have a list of elements: {{1, 2}, {1, 5}, {2, 6}, {3, 7}, {4, 8}, {5, 6}, {5, 9}, {9, 13}, {10,11}, {11, 12}, {11, 15}, {15, 16}} I have to divide it into ...
6
votes
2answers
275 views

Efficient setting of properties of multiple vertices in Graph

The functions SetProperty and PropertyValue can only set a single property of a single vertex, as far as I know. How do I set a ...
6
votes
1answer
136 views

Property assignment on a graph vertex using PropertyValue does not work inside a function

I created this function: AddStone[board_Graph, v_, s : white | black | empty] := PropertyValue[{board, v}, VertexState] = s This function should change the ...
14
votes
3answers
480 views

Determining all possible traversals of a tree

I have a list: B={423, {{53, {39, 65, 423}}, {66, {67, 81, 423}}, {424, {25, 40, 423}}}}; This list can be visualized as a tree using ...
7
votes
2answers
428 views

HighlightGraph with different styles

I want to highlight two different directed paths on a graph with two different style. I am using the following two code snippets: ...
4
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1answer
234 views

Removing edge weights from a Graph

How can I remove EdgeWeights from a Graph without affecting any other properties of the graph? Let's construct a graph with ...
5
votes
3answers
628 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 ...
18
votes
2answers
731 views

Graph layout on a grid

Is it possible for Mathematica to layout a graph so that the connections lie on a grid? Furthermore, for graphs with multiple edges per vertex, is it possible to specify the location on the vertex ...
42
votes
2answers
9k views

How can I use Mathematica's graph functions to cheat at Boggle?

This question is inspired by a Stack Overflow question that I decided to solve using Mathematica. In addition to Mathematica, I thought I'd use some of the new version's graph-related functionality, ...
4
votes
1answer
1k views

Is it possible to generate a Hasse Diagram for a defined relation?

I'm looking for a way to create a Hasse Diagram from a given partial order binary relation. The relation will be given explicitly, for example: ...
18
votes
1answer
385 views

How to visualize large graphs with directed edge bundling

I'm wondering if anyone has implemented edge bundled graph plotting? http://www.win.tue.nl/~dholten/papers/forcebundles_eurovis.pdf
3
votes
3answers
772 views

How to draw a directed graph with arrows showing vertically from bottom to top

If I have a directed graph, how can I draw it with arrows pointing vertically from bottom to top, like showing a class inheritance pattern in OOP(object oriented programming)?