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
votes
2answers
64 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
248 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
58 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
70 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
286 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
442 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
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
votes
1answer
616 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
81 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
647 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
521 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
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
180 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
59 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
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
32 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
371 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
136 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
245 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
votes
1answer
162 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: ...
2
votes
0answers
331 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 ...
7
votes
1answer
109 views

Setting PropertyValue for VertexWeight is not persistent

Bug introduced in 9.0.1 or earlier and fixed in 10.0 ...
9
votes
2answers
254 views

Self-loops in Graph may not display correctly or export correctly to PDF (due to BezierCurve problem)

Bug introduced in 10.0 and persisting through 10.3 Problem is due to a BezierCurve bug. I don't understand why the following does not work: ...
6
votes
0answers
65 views

VertexDelete not working on graph with VertexWeight

Bug introduced in 10.0 and fixed in 10.3 Good afternoon, I have observed an "unexpected behaviour" with VertexDelete and a graph with vertex weights. This is a minimal working example: OK ...
12
votes
0answers
180 views

A question about weighted graphs

Bug introduced in 8.0 or earlier and persisting through 10.3 I need create a weighted graph with given data. Number of nodes: $53$ $\quad$ Number of edges: $91$ ...
1
vote
0answers
112 views

GraphDistance gives incorrect result in weighted multigraph [closed]

Bug introduced in 10.0 and persisting through 10.3 Multigraph support was introduced in 10.0 There are bugs in Graph on Mathematica 10.1. For example, ...
18
votes
1answer
215 views

Systemic bugs in GraphPlot and related functions such as TreePlot and TreeForm

Bug introduced in 7.0.1 or earlier and fixed in 10.3.0 I believe I have come across a rather curious bug in TreeForm: ...
12
votes
2answers
428 views

Determining whether two $k$-chromatic graphs are isomorphic (respecting vertex coloration)

Consider the case where I have two $k$-chromatic graphs $G_1$ and $G_2$, i.e. two graphs where individual vertices can be colored with one of a set of $k$ total colors, and I would like to determine ...
1
vote
1answer
34 views

Scan appears to work setting graph properties, but get error on property-read

This is a self-contained version of something a bit bigger - going for brevity. It is a bit synthetic, but there are applications I have in mind where the {{1,2}} will be replaced with real data, more ...
2
votes
1answer
50 views

Path with no dependence violations

I am guessing this will be a duplicate(it seems like a common task), but I obviously can't find the right page. I have a directed graph showing dependencies, and I want to list the vertices in an ...
2
votes
1answer
105 views

Finding nonequivalent 3-cycles and edges of a given graph

So I have three graphs defined by the following nested list, I'm using this list notation instead <-> notation because it is more convenient for another part ...
2
votes
2answers
164 views

How to find all possible paths with as many edges between two same vertices?

Suppose I have an undirected graph G = Graph[{1 <-> 2, 2 <-> 3, 2 <-> 3, 3 <-> 4}] I used ...
6
votes
2answers
224 views

Extract bibliography from a PDF document

I am trying to extract bibliographies from academic papers which are in pdf format, and I have to do this for 100+ papers. My goal is to create a network of citations amongst the authors and identify ...
6
votes
2answers
164 views

Grouping the list of numbers that have common.

I am working on some simple problem. It is like puzzle.. Let's say I have some list input={{1,1},{1,2},{1,3},{2,3},{3,3},{4,4}} Which means 1 can go and back to ...
5
votes
0answers
130 views

Number of 4-colorings of Johnson solids

I want to know the number of 4-colorings for all Johnson solids. This is equivalent to evaluating the flow polynomial for the corresponding polyhedral graphs at $k=4$. I tried the following to get ...
8
votes
1answer
86 views

Is there an easy way to set or retrieve a graph edge properties as a list, in a single go?

I am trying to use arbitrary edge properties in Graphs, and I am looking for easy ways to work with them. In many cases it would be convenient to be able to set ...
4
votes
1answer
84 views

How to use the “EdgeLayout” suboption of GraphLayout?

According to the documentation, GraphLayout has an EdgeBundling suboption, which can take the following values: ...
0
votes
1answer
75 views

Creating confidence interval plots for random graphs

I have the following code where I create instances of random graphs and use their properties to compute the mean of a quantity labeled 'PoA'. In the last line, I use a range of values for the ...
1
vote
0answers
53 views

Graph equivalent of GraphPlot's MultiEdge style?

I like the default display of Graph much better than that of GraphPlot, but I do not see how to turn off the use of multi-edges ...
0
votes
3answers
122 views

How to Change Vertex List in a Grid Graph

I would like to actually change the vertices in a grid graph instead of simply changing the label. Ultimately, I want the vertices to be points on a plane. So if given a simple grid graph ...
1
vote
1answer
72 views

LayeredGraphPlot how to change color of vertex box

For LayeredGraphPlot how to change the default yellow color? ...
2
votes
2answers
181 views

VertexLabelStyle not found in Mathematica 8.0.0.0

I tried to use VertexLabelStyle, but seemed not recognized in my system with version number 8.0.0.0. Is this expected or I have missed something? From the online ...
2
votes
1answer
59 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: ...
4
votes
1answer
95 views

Is there a way to efficiently generate a large “incomplete” k-partite graphs

A complete k-Partite graph can be divided into "k" distinct sets of nodes, each of which is connected to all nodes not in its own set. This can be generated with code CompleteGraph[{an, bn, cn}] ...
0
votes
3answers
103 views

Weighted and directed network computation in Mathematica

Is there any set of commands in Mathematica to compute mean shortest path, global clustering coefficient, diameter and radius of the network, etc. for weighted and/or directed graphs? There indeed ...