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
votes
2answers
75 views

How-to let user define a set of VertexCoordinates in a Graph

Here is a simple code I wrote to visualize what I am trying to achieve: C.1 ...
1
vote
1answer
60 views

Unexpected AdjacencyMatrix output [duplicate]

I have a directed graph with this Edgelist defined as follow: ...
2
votes
2answers
72 views

Recursive graph expansion and rewiring

I want to take this graph and convert it into this graph by repeatedly substituting each of its nodes according to this rule After loading the initial graph and the substitution rule ...
25
votes
2answers
3k views

How to plot planar graphs as such?

A planar graph is a graph that can be drawn in the plane such that no two edges cross. For example, the graph ...
1
vote
1answer
81 views

How do I customize vertex label texts in tree plot correctly?

By the following code TreeGraph[{1, 2, 3}, {1 -> 2, 1 -> 3}, VertexLabels -> {"a", "b", "b"}] I get . This is incorrect. I need "a" to label the vertex ...
4
votes
1answer
88 views

How can I change VertexWeights in a Graph?

Bug introduced in 9.0 or earlier and fixed in version 10.0.0 I evaluate ...
4
votes
1answer
126 views

Is there really a bug in the following code, taken from the reference documentation for PetersenGraph?

Bug introduced in 9.0.0 and fixed in 10.0.0 PetersenGraph[5, 2, EdgeLabels -> {8 \[UndirectedEdge] 9 -> "hello"}] appears to evaluate perfectly, as ...
11
votes
3answers
548 views

Mathematica 10 Graph issue

Bug introduced in 10.0.0 and fixed in 10.0.2 Please try to evaluate this code in Mathematica 10. ...
1
vote
2answers
139 views

Styling the edges of a graph according to the multiplicities of the edges

I used the following code to make a simple triangle, in which the nodes have different effects each other: ...
6
votes
0answers
64 views

Functionality of FindMaximumFlow

I know that the superseeded function NetworkFlow (needs Combinatorica) uses Goldberg-Tarjan's Push-Relabel-Algorithm but i cant find any information on Mathematica's built-in-function (...
2
votes
0answers
75 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 ...
1
vote
1answer
91 views

How to find a cycle with a property in a graph

Let's have a graph with this edge list: edgelist = {s -> 1, s -> 2, 1 -> 3, 2 -> 1, 2 -> 4, 3 -> 2, 3 -> t, 4 -> 3, 4 -> t}; I want ...
1
vote
1answer
64 views

calculate relationship between cause and effect (rows/columns/delta etc.) on tableform

I tried to enter this Excel (on the right of the picture) information to program. following these codes has been used: ...
6
votes
2answers
99 views

Delete vertices of degree 2 and rewire graph

I want to delete all vertices of degree 2 from a graph and rewire it. Given a graph like graphA, I want to obtain graphB. ...
13
votes
2answers
344 views

Why is NeighborhoodGraph so slow?

To get neighboring vertices I first tried: gg = GridGraph[{10, 10, 10, 10}]; VertexList[NeighborhoodGraph[gg, 1, 1]] // AbsoluteTiming {5.539308, {1, 2, 11, ...
3
votes
2answers
179 views

CommunityGraphPlot doesn't size

Bug introduced in 9.0 and fixed in 9.0.1 When I need to plot a 'large' graph with CommunityGraphPlot the output is always sized at the Mathematica default value. The Graph object itself can be ...
4
votes
1answer
153 views

References on functions FindGraphPartition and FindGraphCommunties

Does somebody have some interesting references on the FindGraphPartition and FindGraphCommunties[.., Method -> "Spectral"] ...
0
votes
1answer
58 views

How to check if (u,v) and (v,u) edges are in a given directed graph

I have a graph and i want a module to run through all the edges of this graph and check whether (u,v) edge is in this graph and (v,u) edge is in another given graph.
5
votes
1answer
95 views

How to create a MorphologicalGraph from MorphologicalBranchPoints

I want to select the morphological branch points of a thinned image to create a MorphologicalGraph like the one obtained by Pruning. I want to avoid the pruning step. How can I delete from the ...
3
votes
2answers
98 views

Coloring network edges by weight using GraphPlot

Following up on a previous question about how to color the nodes (vertices) of a network (graph) according to a color scaling of a property of those nodes, I'm now asking basically the same thing ...
8
votes
2answers
187 views

Efficient solution for a discrete assignment problem with pairwise costs

Let's consider a simple graph with N vertices, and a corresponding set of N items. The goal of the problem is to assign every item to a vertex on the graph so that sum of a per-edge (that is ...
10
votes
2answers
635 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: ...
0
votes
0answers
32 views

Weighted graph vizualization [duplicate]

Is it possible to visualize a weighted graph, so lines on screen would reflect weight? I.e., be longer, or shorter depending on edge weight? Slight OT: which graph visualising libraries/tools can do ...
23
votes
2answers
1k views

Drawing pairs (planar graph, circle packing)

Circle packing theorem states: For every connected simple planar graph G there is a circle packing in the plane whose intersection graph is (isomorphic to) G. How to use Mathematica to draw examples ...
9
votes
1answer
137 views

FindHamiltonianCycle is not invariant to edge permutation

Bug introduced in 9.0.1 or earlier and fixed in 10.0 Found this bug-like behaviour today: if the order of edges is changed so that VertexList does not return the ...
0
votes
1answer
39 views

How to perform operations with vertices from any edge on a Graph object

I'm trying to get the vertices from an large list of edges on a Graph object in Mathematica 10. I need to operate them, adding, substracting dividing. As an ...
0
votes
0answers
49 views

Why does (Layered)GraphPlot lose labels and renumber vertices?

I define a graph of numbers as vertices, but also labeled, like g=Graph[{Labeled[1 \[DirectedEdge] 5, "text1"]…},VertexLabels -> {79 -> "text2",…}]. This is ...
2
votes
1answer
62 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 ...
5
votes
1answer
169 views

Arbitrary shape GridGraph

There is a function GridGraph that generates a finite square lattice graph. Is there a way to make a generalized solution (e.g. with hexagons, or triangles instead of squares)? To put it in more ...
2
votes
2answers
62 views

Network Graph: show highly connected components

I want to create a network graph without the small subgraphs which are disconnected from the big network graph. Suppose I want to visualize the edgelist: ...
2
votes
0answers
84 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}, ...
1
vote
1answer
40 views

Can I rely on the ordering of the adjacency matrix? [closed]

Suppose I have created a Graph[{1,2..n}, {1->3, etc}], and I take the adjacency matrix of that graph. Can I rely on the fact that the i-th entry in the graph is the i-th node in the matrix? Or maybe ...
1
vote
0answers
84 views
2
votes
3answers
166 views
3
votes
1answer
42 views

How can I get the vertex labels of an existing graph?

For example, if there is a graph g = CompleteGraph[5, VertexLabels -> {1 -> "v1", 2 -> "v2", 3 -> "v3", 4 -> "v4", 5 -> "v5"}] How can I later ...
0
votes
1answer
71 views

Compute complete graph and make minimum spanning tree

I'd like to plot a complete Graph and then compute the Minimum spanning tree of it. I already can make a complete graph out of a list that countrydata gives me: ...
4
votes
2answers
92 views

Iterative Tree Plot for the Sum of an Integer's Digits Squared

I am trying to make a graph that depicts integers<100 mapping to the sum of their digits squared. I can do this for one iteration, but I don't know how to do it for more than one, or until the new ...
1
vote
2answers
85 views

What is the correct way to assign and use properties of vertices in graphs?

I'm using Mathematica 10, but I'm having a hard time getting it to do anything useful for network analysis because I'm having a hard time working with node properties and analyzing the graph by its ...
4
votes
2answers
63 views
6
votes
1answer
96 views

Slow-down encountered for RandomChoice in large lists

I was wondering if anyone could help me to speed up this code snippet which creates simple (sparse) networks by preferential attachment. The algorithm adds a vertex and an edge each time interval. ...
1
vote
1answer
141 views

Computing Domination Numbers of Graphs

Is there a way to get Mathematica to compute the domination number (size of the smallest dominating set) of a graph? There doesn't seem to be a direct command for this, so I'm not sure if there would ...
1
vote
0answers
47 views

reset the value of a variable [closed]

Folks, I have a problem in populating a matrix without overriding the values. After performing computations for various values for j, I want to store these values in following matrix. Here is the ...
0
votes
0answers
69 views

Shortest Common Superstring for all k-length strings on an alphabet

Given all strings of length $k$ of an alphabet of size $n$. This gives $n^{k}$ strings. Now I want to create one superstring that contains all these strings as substrings. They hopefully strongly ...
6
votes
1answer
267 views

Efficiently find all connected subgraphs

Is there a way to generate all the connected subgraphs of a graph in mathematica without going through all the subsets of the nodes and checking if the subgraph is connected (which will be ...
2
votes
1answer
425 views

Display a labeled multigraph

Introduced in version 9, fixed in version 10. Thanks Szabolcs for providing this screenshot showing that the bug is fixed. Despite the integration of graphs and networks, multigraphs are ...
2
votes
1answer
230 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 ...
4
votes
1answer
65 views

Why does TreePlot ignore the vertex labels in a TreeGraph argument?

Example (watch the vertex labels): aTree = TreeGraph[{"a" -> "b", "a" -> "c"}, VertexLabels -> "Name"] ...