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

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1answer
100 views

Visualizing Matrix that represents a network

I have a nxn matrix $A$ that represents a network. I have $n$ nodes in the network, and the matrix $A$ represents the number of connection (edges) between the different nodes. For example, if $A$=0, ...
6
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1answer
116 views

Networkgraph, Thickness of edges based on calculated values

On this blogsite I've read a interesting blog about visualising a correlation matrix. So I started with a simple file like: ...
26
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2answers
2k views

Trying to Visualize a Collatz - The Collatz conjecture

I happen to have this collatz collatz[x_, y_] := If[x == 3*y || x == 2*y + 1 || y == 3*x || y == 2*x + 2, 2, 0] So i want a visual 3D adjacency graph of my ...
1
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1answer
87 views

Labeling the vertices of a graph

I would like to label the vertices of a complete graph alphabetically. But I am stuck because I don't know how to associate only one vertex to a letter. ...
1
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1answer
44 views

Medium-sized graph won't build

Why can't Mathematica import a 40-KB file (mediumEWD.txt) and build the underlying graph in some decent time? I waited a minute, nothing. ...
13
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3answers
622 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 ...
2
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1answer
57 views

Highlighting a graph with non-trivial vertex definitions

When defining a graph whose vertices are sets e.g. the Kneser graph, how does Mathematica interpret the vertices? I am having trouble highlighting vertices when I define vertices with sets, but for ...
1
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1answer
69 views

Vertices overlap with vertex labels

How to prevent a behavior on a picture below? Why vertices overlap with vertex labels? ...
0
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1answer
54 views

How to change vertex font size in TreeGraph?

I tried to change vertex label font size by the following code ...
4
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1answer
82 views

How do I change one edge in a tree graph to a double arrow?

I use the following code plot a binary tree and wants to change an edge to double arrow. ...
6
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1answer
320 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 ...
2
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1answer
220 views

Draw a de Bruijn graph with random vertex size

I am trying to draw a graph that looks like below, This the code I have so far, ...
0
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1answer
73 views

Getting error from CommunityGraphPlot

Situation I'd like analyse my web site with CommunityGraphPlot as follows: Step 1: Define a function to scrape the all the webpages from expected website. ...
3
votes
1answer
87 views

Deleting isomorphic graphs efficiently

I'm trying to delete isomorphic graphs from a large list. My solution is as follows: DeleteIsoG1[gl_List]:= Module[{}, DeleteDuplicates[gl,IsomorphicGraphQ]]; ...
14
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2answers
536 views

Listing subgraphs of G isomorphic to SubG

If I have an undirected graph G, how could I write a function in Mathematica to obtain a list of subgraphs of G that are isomorphic to some other undirected graph SubG? I'd like to learn how to ...
2
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1answer
68 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 ...
3
votes
1answer
73 views

Cannot get Mathematica to recognise Vertex Weights of Graph

I am using Mathematica Version 8.0 I've tried variations of the following commands, in order to assign the weight $1/k$ for vertex $k$, for a graph defined on {1,2,..,n} via the edge rule $$(k,k') \...
25
votes
5answers
4k views

How to get graph layout that reflects edge weights?

My heart soared to discover that Mathematica 8 offers support for specifying a weighted adjacency matrix in WeightedAdjacencyGraph. But it seems that, regardless of the weights between edges, the ...
5
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1answer
287 views

Tools for finding minimal or almost-minimal graph vertex colorations in Mathematica v9?

I'm looking to compute minimum vertex colorations (s.t. no two vertices of the same color share an edge: http://en.wikipedia.org/wiki/Graph_coloring) for graphs in Mathematica v9 with potentially up ...
3
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1answer
78 views

Generate all directed graphs with n vertices, + additional constrains

I have a problem similar to Using GraphData to generate all directed graphs with n vertices. That is, I want to have all directed graphs with n vertices (particularly, for n = 4). However: not up ...
8
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1answer
97 views

Smallest connected subgraph containing all given vertices

Given a connected graph $G$ and a subset of its vertices, $S$, I need to find the smallest connected subgraph of $G$ containing all of $S$. How would you approach this in Mathematica? I am asking ...
3
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2answers
144 views

How do I find all cut vertices (aka articulation points) in a graph?

Given a connected graph $G = (V,E)$, we say that a vertex $v \in V$ is a cut vertex of $G$ if the removal of $v$ from $G$ causes $G$ to become disconnected. How can I find all cut vertices of a given ...
2
votes
3answers
91 views

network visualization with different colors for different edge labeled

I have a network with 3 different edge types, edgelist file is a three column file with id1, id2 and edge label. I uploaded the file here What I need know is to find a way to plot this network, as ...
4
votes
2answers
113 views

How to plot a graph with some disconnected vertices?

I am trying to plot a graph with $6$ vertices but I do not want some of the vertices to be connected. I have drawn a picture to illustrate my problem. So far I know how to plot $6$ vertices without ...
4
votes
1answer
284 views

Why don't the arrowheads show for this directed graph?

Bug introduced in version 9.0 or earlier and fixed in 10.3 It's very weird, but the first graph is shown as undirected (dots connected by lines, not arrows. The second is shown as directed, with ...
1
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1answer
54 views

what causes this display problem (missing arrows) with this adjacency graph [duplicate]

AdjacencyGraph[{{1, 1, 0}, {0, 0, 1}, {0, 0, 1}}, DirectedEdges -> True] If you look very closely at the resulting visual display in a notebook (below), you ...
7
votes
2answers
315 views

Is there something akin to “SubgraphIsomorphismQ” in Mathematica 9?

Provided two unlabeled graphs, $G$ and $H$, I would like to test where $H$ is a subgraph of $G$. In other words, I'd like to test whether we can prune some fixed number of vertices or edges from $G$ ...
3
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2answers
63 views

Spatial Display of “Union of Geodesics” in a Random Geometric Graph

After reading.... Finding all shortest paths between two vertices which addresses an important topic in Mathematica graph visualisation, I use ...
5
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1answer
240 views

Finding a complete subgraph efficiently

I'm working on some experimental algorithms which would benefit from methods to find an instance of complete subgraphs with N vertices in an undirected graph. This far I've tried these methods: <...
1
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0answers
57 views

Visualizing site map using a Tree

I've been trying to visualize a sitemap for analysis purposes. So far, using Leonid Shifrin's makeTreeRojo function, I've been able to build a somehow decent visualization. First, I fetch and format ...
2
votes
1answer
68 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 ...
10
votes
3answers
273 views

Custom edge style (e.g. brush stroke, writing ink, etc.)

I would like to draw a graph with Mathematica in such a way that it looks like a handmade drawing or painting. To be more precise, is there a way to set a custom edge style such that it looks made ...
5
votes
1answer
439 views

Counting paths of a certain length between a source and sink vertex

I have a graph $G$, which may be directed or not, and I was wondering if there was an efficient way of using, say, BreadthFirstScan[] and FindShortestPath[] to count the number of paths between some ...
1
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0answers
43 views

Depth limited search in mathematica

I often use FindPath[G, 1, 2, {L}, All] where $G$ is some graph. This finds all paths of length exactly $L$ edges which run between nodes $1$ and $2$. In large ...
28
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1answer
600 views

Visual representation of a Ranking over time (image provided)

[Disclaimer: I initially posted this question on stackOverflow 2 months ago and think it might be better suited for this forum (link to original question)] The graph below shows a ranking of ...
1
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0answers
80 views

Mathematica in Action (Wagon) — code to generate a great circle is giving error [closed]

I have code from Stan Wagon's Mathematica in Action, Chapter 17 (Great Circle Problem), but when I try to run it, it does not work. I have Mathematica 10. The code that does not run is shown below. Do ...
4
votes
1answer
625 views

Isomorphisms for graphs with loops and multiple edges

I am working with graphs with multiple edges and loops, and I want to eliminate all isomorphic graphs from a long list I've generated. The FindGraphIsomorphism ...
17
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1answer
488 views

Import and Plot Git Commit History

What might be the easiest to import and plot all commit history for a github project? I'm looking for something similar to the following.
1
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0answers
52 views

How to set distance between connected vertices in graph?

I'm new at making graphs in mathematica 9, so I don't know if this question is contained in some of already asked ones. I started making it to visualize a polytope, which is build by a sertain ...
4
votes
1answer
170 views

Fast way to get edge-list of graph in terms of vertex indices (not vertex names)

I am looking for the fastest way to achieve the following: Given a Graph, retrieve its edge list in terms of vertex indices (not actual vertices). For example, ...
3
votes
0answers
58 views

How best to use or to emulate the “obsolete” Combinatorica command Contract?

The obsolete Combinatorica package has a command Contract for contracting an edge in a graph. Below is my very clunky attempt to work with up-to-date graph objects ...
21
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2answers
1k views

How can I conveniently call igraph from Mathematica?

Mathematica has lots of functions for working with graphs and networks, but there are still some functionality holes that are provided by other packages. Also, due to the nature of graph theory, ...
3
votes
1answer
54 views

TreePlot: arrows on specific lines

I have the following list of rules: L={1->2,2->3,3->3}; and I want to plot a tree graph: ...
1
vote
1answer
31 views

WeaklyConnectedGraphQ evaluates to False. Is this the expected result?

Take the simple graph {1->2, 2->3, 3->1}: TreePlot[{1->2,2->3,3->1}] I would expect that ...
8
votes
2answers
370 views

Is there a bug in FindClique?

If h is a graph, FindClique[g, {n}] should return a clique on exactly $n$ vertices if one exists in ...
6
votes
2answers
135 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 ...
11
votes
2answers
244 views

Finding the minimum vertex cut of a graph

Bug introduced in 9.0.1 or earlier and fixed in 10.2.0 Note: FindVertexCut is new in 9.0. It seems that Mathematica is not correctly finding the smallest set of ...
5
votes
3answers
1k views

Fast code to generate large random graph with fixed degree sequence

I'm trying to create a function so to generate large random graph with a fixed degree sequence $\{v_1,v_2,\dots,v_N\}$, where $N$ is the number of vertices in the graph. The Mathematica function that ...
5
votes
3answers
1k views

How to find all graph isomorphisms in FindGraphIsomorphism

I found the second definition of the function FindGraphIsomorphism not working. Here's the definition Mathematica 8 gives: ...
3
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1answer
153 views

IsomorphicGraphQ giving an error when the graphs contain multi-edges [duplicate]

If I run IsomorphicGraphQ on the following graphs, I get an error I don't understand: ...