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
80 views

Checking connectedness of a graph

I am trying to use the Combinatorica package in a Mathematica version 8 in the following code: ...
7
votes
1answer
223 views

Visualize a tree structure using TreeGraph

I have a code that generates a tree of graphics objects. The structure can be visualized like this, with each Rule constituting a parent child relationship: ...
5
votes
1answer
382 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 ...
4
votes
1answer
105 views

How to impose control over vertex-to-vertex Graph edges?

I’m working on a Markov Chain and hope there is a way to impose control over how Mathematica places edges to connect vertices in a Graph. My Markov Chain currently consists of 4 vertices with 2 of the ...
8
votes
3answers
247 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
80 views

Signed Graph from positive and negative correlations

I want to create a signed graph where the edges of my graph are either green (for a positive correlation) or red (for a negative correlation). I only managed to create a graph from a tresholded ...
2
votes
1answer
117 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
343 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 ...
1
vote
1answer
105 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 ...
2
votes
2answers
139 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
245 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
197 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 ...
7
votes
1answer
259 views

Adding/deleting weighted edges to a weighted graph

How can I add and delete weighted edges in a weighted graph? Using Graph in Mathematica I want to add a weighted edge to a weighted graph. The problem is ...
1
vote
0answers
168 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). ...
0
votes
1answer
139 views

Subset of edges with a different color

I want to color a subset of the edges of my graph with a different color. My graph currently has a large number of edges, so the following is just a toy example ...
18
votes
1answer
396 views

How to visualize large graphs with directed edge bundling

I'm wondering if anyone has implemented edge bundled graph plotting? http://www.win.tue.nl/~dholten/papers/forcebundles_eurovis.pdf
2
votes
1answer
95 views

What is the best way to save a large graph object, allowing it to be reloaded quickly in a new kernel?

I generated a very large graph, too large to simply display and manipulate with copy/paste operations. How can I somehow save the graph to a file to allow it to be rapidly reloaded after I quit out ...
7
votes
1answer
325 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
129 views

Deleting Vertices in GridGraph

Take a simple GridGraph: g = GridGraph[{3, 3}, VertexLabels -> "Name", ImageSize -> 150, ImagePadding -> 10] I am ...
4
votes
2answers
176 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: ...
3
votes
2answers
205 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 ...
2
votes
1answer
231 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 ...
4
votes
2answers
158 views

Total weight of a graph

I need to find the total weight of an WeightedAdjacencyGraph. I have a graph in that form ...
0
votes
1answer
121 views

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

I have a list of edges defined based on vertices like this: ...
0
votes
1answer
64 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
137 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
295 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 ...
22
votes
2answers
3k views

How to play with Facebook data inside Mathematica?

I saw this post from Wolfram here and I would like to know how to import facebook data into Mathematica.
3
votes
2answers
163 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: ...
1
vote
1answer
104 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
1answer
277 views

Generating a graph object where vertices are pixel coordinates and edges represent two pixels being in the same Moore neighborhood

I have a list of integer pixel positions, pts, and I wish to create one or more graph objects where vertices at these pixel positions share an edge if they are ...
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
183 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 ...
15
votes
3answers
229 views

What is the most convenient way to change options for Graph[] objects?

What is the most convenient way to change options such as VertexLabels in existing Graph objects? (Version 7 users note: ...
13
votes
4answers
433 views

How to recompute the layout of a Graph?

I asked a question about changing Graph properties in a similar way to how Show can change ...
2
votes
3answers
395 views

GraphPlot only working when I evaluate twice

I have some code that builds a graph and some vertex coordinates, but when I evaluate it I get a message that the list of coordinates is not valid and the graph is not valid and it shows the output as ...
2
votes
1answer
158 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
145 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
184 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
60 views

GraphHighlightStyle with multiple datasets

I am trying to highlight several subgraphs of a graph using the following command: ...
5
votes
1answer
197 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
111 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: ...
4
votes
3answers
710 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 ...
3
votes
3answers
287 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
128 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 ...
4
votes
3answers
612 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: ...
2
votes
0answers
55 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
121 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
71 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. ...
1
vote
2answers
328 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 ...