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

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3
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1answer
103 views

What exactly does LocalClusteringCoefficient compute for directed graphs?

For undirected graphs, the LocalClusteringCoefficient of vertex v is ...
6
votes
2answers
62 views

How to specify custom graph styles for `GraphStyle`?

There is a way to specify custom themes for plots (Is it possible to define a new PlotTheme?), but themes to not apply to Graph objects, not even to ...
1
vote
3answers
55 views

How to draw graph with named vertices by adjacency matrix?

I have the adjacency matrix of graph and I want visualize this graph. I tried: ...
10
votes
1answer
396 views

Shortest tour with vertex priority

I changed the title of my question and tried to simplify formulation of the problem. I solve a very big vehicle routing problem. I divided this one big problem on many small sub-problems. Each small ...
1
vote
1answer
96 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
votes
1answer
111 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: ...
25
votes
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
vote
1answer
74 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
vote
1answer
42 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
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 ...
2
votes
1answer
55 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
vote
1answer
60 views

Vertices overlap with vertex labels

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

How to change vertex font size in TreeGraph?

I tried to change vertex label font size by the following code ...
4
votes
1answer
81 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
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 ...
2
votes
1answer
212 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
votes
1answer
70 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
81 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
votes
2answers
522 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
votes
1answer
54 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
66 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') ...
24
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
votes
1answer
263 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
votes
1answer
73 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
votes
1answer
92 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
votes
2answers
130 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
89 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
100 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
280 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
vote
1answer
52 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
312 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
votes
2answers
59 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
votes
1answer
137 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
vote
0answers
54 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
61 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
247 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
425 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
vote
0answers
39 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
votes
1answer
582 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
vote
0answers
78 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 ...
3
votes
2answers
189 views

How to compute the automorphisms of graphs with multiple edges?

I try to compute the Automorphisms of graphs with multiple edges from its AdjacencyMatrix but failed. The following code shows ...
4
votes
1answer
608 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
votes
1answer
464 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
vote
0answers
47 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
143 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
57 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
votes
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
51 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
29 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
365 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 ...