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

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4
votes
1answer
157 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, ...
1
vote
1answer
67 views

LayeredGraphPlot how to change color of vertex box

For LayeredGraphPlot how to change the default yellow color? ...
2
votes
0answers
81 views

How do I get all possible paths in terms of edges, and not vertices in Mathematica?

Suppose I have an undirected graph ...
0
votes
3answers
110 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 ...
2
votes
1answer
58 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
86 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}] ...
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 ...
0
votes
3answers
98 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 ...
11
votes
1answer
136 views

How can I route edges manually for a Graph?

Most graph layouts supported by Mathematica use straight lines for edges; or at least something that only depends on the coordinates of the two adjacent vertices of the edge and nothing else. A ...
0
votes
1answer
180 views

Network/Graph Visualization read edgelist

I have what it seems to be a very trivial question, but after searching for hours I was not able to find an answer, so I am asking here. I have an edgelist for a graph, a 2 column csv file with ...
17
votes
1answer
475 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.
8
votes
0answers
88 views

More efficient way to generate lattice graph with edges between visible vertices?

Given a nXn lattice, I need to generate the graph such that there is an edge between two vertices iff they are directly "visible" to each other, i.e., there is no vertex between them. I'm using ...
2
votes
1answer
48 views

Converting from GraphData to graph object

I know this is a simple question, but suppose I have a graph G = Part[GraphData[n],i] How do I convert this into a graph object accepted by ...
1
vote
1answer
91 views

Lack of arrows in Markov Chain graphs

I'm following this: http://www.wolfram.com/mathematica/new-in-9/markov-chains-and-queues/structural-properties-of-finite-markov-processes.html When I try to graph the Markov chain with Graph[proc] I ...
1
vote
2answers
64 views

How do I import a non-directed graph in graphml format?

I have created a graph with undirected edges, and I'm trying to import it into Mathematica. However, when I import it, I get directed edges. ...
2
votes
1answer
45 views

Increasing the font size in the Vertexlabels of GraphPlot

I have the following code and corresponding output: GraphPlot[Table[i -> Mod[3^i, 5], {i, 20}], VertexLabeling -> True] I wish to do two things: 1) ...
1
vote
1answer
34 views

Display options for GraphData output [duplicate]

How can the display of graphs using GraphData be customized? For example, how can we customize the vertex style, color, edge thickness of the output to...
9
votes
1answer
72 views

Cannot set VertexCoordinates twice in a Graph. Workaround?

Versions 10.0-10.2 seem to have a bug when trying to set VertexCoordinates twice on a graph (version 9.0 is fine). Can you confirm it? What is a good workaround ...
5
votes
1answer
228 views

Adjacency matrix from image file of plane map

I have image files (PNG format) of plane maps of regions delimited by black borders I would like Mathematica to compute the associated adjacency matrix for the contiguous regions in these maps. ...
0
votes
0answers
61 views

adjacency matrix with directed graph connected nodes

I was trying to plot a 9x9 adjacency matrices which produce a useless directed graph. Codes for that I used: ...
0
votes
0answers
85 views

ViewVector requires click before behaving with Graph3D (Also, viewing 3D subgraph “head on.”)

I want to produce 3D subgraphs that looks "head on" at the remaining vertices, held in their original positions via VertexCoordinates. The default viewpoint is not ...
2
votes
0answers
37 views

Algorithm to determine if two colored graphs are isomorphic? [duplicate]

I have two (vertex-)colored graphs. I want to determine if they are isomorphic, with the condition that the isomorphism respects the colors of the vertices. Moreover, I want the algorithm to output ...
2
votes
1answer
98 views

Multiple colors on a single graph edge?

Is there any way to put two colors on one single graph edge? For example, I want to highlight two cyclic paths (red and blue). But, if I put the two colorings into one image, it does not work as I ...
1
vote
0answers
105 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, ...
5
votes
2answers
149 views

How to show the direction of highlighted path in graph

I am trying to show the direction of FindHamiltonianPath on the Graph. ...
6
votes
1answer
201 views

Vertex Order of Graph

Given a graph, I want to find the shortest distance between each pair of vertices: ...
6
votes
0answers
99 views

Issues adding properties to multigraph

Unsupported Functionality (loosely, a bug) Mathematica (as of 10.4.1) does not support multi-graph where edge properties vary between two nodes that share multiple edges. Although this is not ...
3
votes
2answers
86 views

How to specify different colors for edges going between the same two vertices in Graph?

Here is an example: edge1 = Property[1 -> 2, EdgeStyle -> Red]; edge2 = Property[1 -> 2, EdgeStyle -> Blue]; Graph[{edge1, edge2}] This does not ...
1
vote
1answer
61 views

Unexpected AdjacencyMatrix output [duplicate]

I have a directed graph with this Edgelist defined as follow: ...
2
votes
2answers
79 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
128 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 ...
2
votes
2answers
79 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 ...
6
votes
1answer
235 views

Calculate dual graph of planar Graphics map

This diagram from a Wikipedia article illustrates what I hope to accomplish in Mathematica: I have a planar map in Graphics format. Here are two very simple ...
7
votes
1answer
117 views

How to extract a Graph[] from an image?

This graph (as a picture) is given below: I am wondering rather than setting up this network graph using Mathematica syntax such as PathGraph,...
1
vote
2answers
153 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: ...
1
vote
1answer
69 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
118 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. ...
12
votes
0answers
170 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
1answer
97 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 ...
5
votes
1answer
105 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 ...
0
votes
1answer
64 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.
2
votes
1answer
96 views

Visualisation of feedback loops in a directed graph

Here are the nodes (vertices) of my graph: ...
0
votes
0answers
34 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 ...
3
votes
2answers
118 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 ...
2
votes
2answers
74 views

DiscreteMarkovProcess: labelling of states

Related, but it seems like the respondents there misunderstood the question. The following errors as DiscreteMarkovProcess::invsm: ...
14
votes
1answer
158 views

IsomorphicGraphQ fails to recognize that two empty graphs are identical

Bug introduced in 9.0.1 or earlier and persisting through 10.4.0 Consider the following two graphs: ...
0
votes
1answer
43 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
56 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
67 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 ...