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

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8
votes
3answers
234 views

Pairwise distances of points and classification using GraphDistanceMatrix

The challenge Given $n$ points in $\mathbf{R}^3$ and a cutoff distance, $d$, I would like to determine all pairs of points that are separated by less than the given cutoff distance, $d$, and all ...
2
votes
1answer
110 views

GridGraph layout with added edges

I noticed that the nice symmetric layout of a grid graph gets distorted when additional edges are added to the graph. Is there way to prevent that from happening and to keep the rectangular, grid-like ...
2
votes
2answers
311 views

Generating social network graph from a CSV file

I am new to Mathematica and wanted to generate undirected graph for data sets that show the relationships of organizations with each other. The data is in a square matrix. The cells of the matrix ...
0
votes
2answers
181 views

Generating a random tree of given cardinality, depth, and labeling

For demo, exploration and teaching purposes, I would like to be able (and asking you for help) to generate these special instances of trees: For given: N - number of nodes in the tree D - depth of ...
2
votes
2answers
130 views

Assigning weights to edges of a hypercube based on the Gray code labels for vertices being connected

Say I want to construct an $n$-dimensional hypercube graph $G$ using the command: G = HypercubeGraph[n]. I'd like to assign edge weights to the $2^{(n-1)}n$ edges ...
2
votes
1answer
206 views

Create a graph from KML file

I'm wondering how I can take a .KML (Keyhole Markup Language) file and convert/express it as a graph for use in Mathematica. Even just in general, is it possible to convert a KML file to a graph? I'm ...
1
vote
2answers
193 views

Fast randomization of a graph, while keeping the graph connected

I'm looking for a very efficient method for randomizing graph of a given size (N nodes, L links), but keeping them connected. Assume you have the adjacency matrix A of a given connected graph. You ...
1
vote
0answers
154 views

How to extract connected bipartite graph from incidence matrix

I'm trying to extract a connected bipartite graph Bconn from the a given incidence matrix B- I have a matrix representing a bipartite graph - the incidence matrix B (weighted or not is unimportant). ...
1
vote
1answer
104 views

Reflecting the Polya-Aeppli distribution

How would I go about reflecting the Polya-Aeppli distribution in Mathematica about a y-axis (switching left and right) while keeping the command. The distribution will not allow negative parameters ...
6
votes
1answer
281 views

How to visualize the structure of this dynamic programming code

I am studying Mr. Wizard's answer to this question which tries to identify elementary circles in a graph. That answer uses dynamic programming technique to simplify the code. The underlying guideline ...
1
vote
3answers
120 views

Deleting Vertices in GridGraph

Take a simple GridGraph: g = GridGraph[{3, 3}, VertexLabels -> "Name", ImageSize -> 150, ImagePadding -> 10] I am ...
2
votes
1answer
222 views

Nicely illustrating the evolution and end-state of a discrete-time Markov chain

I'm simulating a discrete time Markov process on a finite state space corresponding to a linear interval $(x_1, x_2, ..., x_N) \in X$, where each time step $t_i$ involves updating the state of some ...
5
votes
1answer
359 views

How to display each step of an A star algorithm?

I wrote a pathfinding program: A*, which is an extension of Dijkstra. I want to see the result of each step at a time. Which function should I use? The main program is the notebook Astar, which is ...
0
votes
1answer
113 views

GraphPlot3D: How to plot undirected graph with a list of edges?

I have a list of edges defined based on vertices like this: ...
4
votes
2answers
171 views

Visualize difference between members of the list

I want to visualize the difference between members of a set: set = {20, 36, 70, 96, 152, 301} This way I get the diffs: ...
0
votes
1answer
62 views

Subgraph, HighlightGraph not acting as expected

I'm trying to create a simple graph from a matrix and then highlight a particular subgraph. My code (simplified from a bigger task) is as follows. I keep getting the "Subgraph::graph: A graph object ...
0
votes
1answer
123 views

How to construct a graph from a list of edges

I have a list of pairs of numbers, representing connections between objects in the real world. Each number is the identifier of an object, there are gaps in the range from the smallest number to the ...
2
votes
2answers
278 views

random geometric graph generation problem

I'm new to Mathematica. I'm trying to generate a random geometric graph in which to have a secure link between any two arbitrary nodes they should share a common key in their key rings (have assigned ...
3
votes
2answers
179 views

Manually adjust graph vertex location by dragging?

Sometimes I have a graph and I want to make tweaks to the vertex locations. Is there any way to manually adjust graph vertex location by dragging? If I double click to edit, I can move around the ...
1
vote
1answer
158 views

Vertex labels versus vertex names in VertexRenderingFunction

The VertexRenderingFunction seems to only use names, not labels. For example: ...
1
vote
1answer
100 views

GraphPlot with black edges no rendering function

Is there any way to make the edges of a GraphPlot black without tediously writing out a long "EdgeRenderingFunction"? I guess you could ask the same kind of question about vertex labeling. For ...
3
votes
2answers
162 views

How to apply GraphLayout to parts of a graph?

I'm trying to sketch polymers. Here is how I do it for the monomer: ...
3
votes
1answer
90 views

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

PetersenGraph[5, 2, EdgeLabels -> {8 \[UndirectedEdge] 9 -> "hello"}] appears to evaluate perfectly, as expected, but in my version 9.0.1.0, the option ...
2
votes
1answer
157 views

Finding a Moore neighborhood connected path of bright pixels along the contour of a text character

I have a simple image, for example a blowup of a Times New Roman character like 'R' saved as a PNG. I then perform the following operations to extract a minimum representation of the contour lines ...
4
votes
1answer
137 views

Dijkstra without Combinatorica

There is some overlap between Combinatorica and the Graph related framework but there are also various elements missing. As far as I can see there is no 'Dijkstra' method or algorithm in Mathematica ...
0
votes
1answer
175 views

Mean path length of randomly generated graphs

I am looking to find the the average path length of 1000 random graphs with the following degree distribution, a few of the vertex degrees are included below ...
1
vote
0answers
59 views

GraphHighlightStyle with multiple datasets

I am trying to highlight several subgraphs of a graph using the following command: ...
5
votes
1answer
194 views

Shortest polygonal path

I'd like to find the shortest distance between some points (every point must be visited), such as between these 3 points: ...
0
votes
1answer
105 views

Connected components of a graph

I am trying to find the number of connected components of numerous named graphs within Combinatorica. The obvious answer seems to be: ...
1
vote
0answers
123 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
3answers
266 views

Generating a graph where vertices correspond to points in an integer lattice and edges connect points less than a threshold distance apart

I'd like to automatically generate a graph where vertices correspond to (and have the coordinates of) points in an $A \times B$ integer lattice, and a graph is generated by connected vertices within a ...
1
vote
0answers
54 views

How to use Automorphisms[] on a graph? [duplicate]

I am having difficulty mixing the new post-Combinatorica graph data structure, with functionality apparently only in Combinatorica. I have constructed a graph using ...
9
votes
1answer
119 views

How to get control over DepthFirstScan?

Is there a way to conditionally take control the flow during a depth-first scan against a TreeGraph? I have a tree graph whose nodes are constructed as object, and there's a method ...
1
vote
1answer
70 views

Assigning Variables for Degree Distribution [closed]

So my code is divided into 3 different sections: 1) Calculating clustering coefficient, 2) Extracting degree distribution 3) Using the degree distribution to get the mean of 1000 networks. ...
2
votes
1answer
174 views

GraphPlot labels overlapping

If I plot the following graph with an EdgeRenderingFunction, the position of both the labels are at dead center, and with a large graph I have the labels completely ...
1
vote
2answers
275 views

Swapping elements of list

Say I have a directed graph inputted in the following format in Mathematica: g = {{1, "a", 2}, {2, "b", 1}} I'd like to plot this graph using ...
1
vote
1answer
116 views

Gradually coloring edges in terms of their vertices colors

In order to color Edges in a Graph after applying a function such as VertexDegree I did the ...
4
votes
2answers
114 views

BezierCurve in EdgeShapeFunction fails when used on multiedges graph

I would like to create a network graph with curved edges. To do this, I wrote this function: ...
4
votes
1answer
154 views

Compatibility issues for Combinatorica package

I am trying to use the Combinatorica package in a Mathematica version 9 in the following code : ...
6
votes
3answers
268 views

Flow in pipeline graph

I have pipeline directed graph which has one source and several sinks ...
8
votes
2answers
229 views

Organise a graph's vertices into levels

I would like to organise a graph's vertices in levels. Consider ...
3
votes
3answers
171 views

Product of edge weights in path

I need to calculate the product of graph edge weights on the path taking into account edge direction. I.e. for graph ...
6
votes
4answers
184 views

Draw graph wherein vertices are ArrayPlots

I need to place ArrayPlots in the vertices of graph. i.e. in graph Graph[{1->2, 2->3, 3->1}] I have to replace vertex 1 with ArrayPlots[{{0,0,1}}] and ...
4
votes
2answers
152 views

Total weight of a graph

I need to find the total weight of an WeightedAdjacencyGraph. I have a graph in that form ...
4
votes
3answers
654 views

Minimum spanning Tree from a weighted adjacency graph

Note: Cross-posted at http://community.wolfram.com/groups/-/m/t/137658?p_p_auth=8QnKtT9I I have a really big graph, 40x40. Here is my code ...
9
votes
3answers
374 views

Remove redundant dependencies from a directed acyclic graph

Given a directed acyclic graph, I want to remove all the edges $v_i \rightarrow v_j$ if $v_j$ is reachable from $v_i$ by some other path. Given the rich set of graph algorithms in Mathematica, what is ...
1
vote
1answer
119 views

Problem with GlobalClusteringCoefficient

I have a simple problem, I would like to measure the global clustering coefficient for a random graph. Here is my code: ...
1
vote
2answers
290 views

Coloring vertices using GraphPlot

I have the following problem: I used GraphPlot to plot my adjacency matrix. I divided my nodes in three groups: ...
3
votes
1answer
178 views

Merging Vertices of a Graph and adding up the edges weights

I have a Weighted Graph of g which looks like this. ...
0
votes
1answer
63 views

Testing Equality Expression?

Even if in Graph[{1 -> 2}] == Graph[{1 \[DirectedEdge] 2}] the answer is True ; but why MMA doesn't show the result of the ...