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
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3answers
539 views

How can one draw a network with nodes and links in a grid shape?

I'd like to be able to use MMa's graphics to make something like this which I know must absolutely be possible (and probably easy) with MMa. I don't actually even need different colors (though ...
8
votes
2answers
1k views

Dynamic graph visualisation using JLink/Java and GraphStream

Visualising the addition of new nodes and edges to a graph to 'watch it grow' is to something Mathematica is not suited to by default. However this type of animation really helps convey the emergence ...
8
votes
3answers
293 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 ...
8
votes
4answers
332 views

Can I stop edges in graphs from drawing on top of the vertices?

Consider the following testadj = RandomVariate[BernoulliDistribution[0.15], {50, 50}]; AdjacencyGraph[testadj, VertexSize -> Large] The nodes are almost ...
8
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2answers
275 views

Organise a graph's vertices into levels

I would like to organise a graph's vertices in levels. Consider ...
8
votes
2answers
367 views

Graphing a network with state transition flows (of varying size)

In one of Stephen Wolfram's recent blog posts (http://blog.stephenwolfram.com/2013/04/data-science-of-the-facebook-world/#more-5350) he provides the network plot below. The size of the arrows that ...
8
votes
2answers
350 views

How do I convert this Nicomachus's Triangle to one with edges?

I want to put edges on this Nicomachus's Triangle r = 7; t = Table[2^(n - k) 3^k, {n, 0, r}, {k, 0, n}]; ColumnForm[t, Center] Is there an easy way to do this? ...
8
votes
2answers
268 views

Cases[data,Colon[key,_]] vs. Cases[data,key:_] toward XPath, XQuery

Exploring methods to index and search tree-structured key:value pairs via named-entity index (key paths) as opposed to Position-based indexing. Using Rule as ...
8
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3answers
439 views

Mathematica 10 Graph issue

fixed in 10.0.2 Please try to evaluate this code in Mathematica 10. ...
8
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3answers
276 views

Preserving labels when using graph functions

I am finding that some functions that accept a graph and return a transformed graph lose all the vertex and edge labels of the graph being transformed. For example, when I define a graph like this: ...
8
votes
1answer
171 views

Using GraphHighlight interactively

I want to build a small GUI, where the user can select either a single edge or a single node of a graph. I got to this point: ...
8
votes
1answer
290 views

How can I sequentially apply different graph embeddings?

Imagine I have some graph G, and I perform a graph embedding using a command like: ...
8
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3answers
443 views

TreePlot with centered vertexes

I want to draw a tree plot for Euler totient function for this question like the following: I generate the EulerPhi for first 20 numbers into a list: ...
8
votes
2answers
521 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: ...
8
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1answer
181 views

Vertex merging in graph?

Given a Graph such as the one produced with the following code ...
8
votes
1answer
786 views

How to add vertex/edge labels to existing graph

If I have already created a graph using Graph. Later, I want to add to the graph some vertex and/or edge labels, how can I do that? Thank you.
8
votes
2answers
169 views

Finding the minimum vertex cut of a graph

Bug present in at least versions 9.0.1, 10.0.2 and 10.1.0 It seems that Mathematica is not correctly finding the smallest set of vertices that will disconnect a graph. Here is an example: ...
8
votes
1answer
503 views

Why does SocialMediaData return such a small FollowerNetwork?

I have hooked up my Twitter account to Mathematica and I have 1468 followers myfollowers = Length[SocialMediaData["Twitter", "Followers"]] 1468 I wondered what ...
8
votes
2answers
311 views

Finding All Chordless Simple Cycles In A Graph

I am doing a research on networks which consists of polygons with different number of sides. I am trying to find all simple cycles in a network which are chordless. As an example, consider the ...
8
votes
1answer
584 views

How can I display a multigraph with different colored edges?

I'm new to Mathematica(version 9) and I'm trying to display a multigraph with different colored edges. Here's my code so far: ...
7
votes
5answers
413 views

Is there a neat way to generate the odd set constraints matrix?

Given a undirected graph $G=(V,E)$, I am trying to generate a related matrix $M$, where columns are indexed by $E(G)$ and rows are indexed by all odd subsets of $V(G)$. I can finish this task using ...
7
votes
2answers
454 views

Convert Graph to Graphics

In Mathematica 9, a graph is returned as an object with head Graph: In[8]:= CompleteGraph[8] // Head Out[8]= Graph ...
7
votes
5answers
575 views

Building graph based on the cities connection?

I built a Graph based on the permutations of city's connections from : ...
7
votes
3answers
2k views

Travelling salesman with start and end points for 30 points

I am doing a route optimisation for delivery vehicles and failing dismally. Please see problem statement below. My current solution uses FindShortestTour, but this does not have defined start and end ...
7
votes
3answers
286 views

Converting Mesh in Density Plots to a Graph

Consider the following line of code: ...
7
votes
3answers
434 views

I can't understand FindShortest Tour

I can't understand the function FindShortestTour because of the result: FindShortestTour[{ {0, 1}, {5, 1}, {2, 1}, {10, 1}}] ...
7
votes
3answers
660 views

Visualizing the output of a Voronoi diagram computation

I need to plot a graph (to be specific: Fortune Algorithm output) with given vertex coordinates and a few unconnected vertices. I am thinking of using Mathematica for that. ...
7
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2answers
995 views

Is it possible to export a graph as graphic to Excel?

It is straightforward to export lists to Excel with Export. Can I export a graphic image, too? This does not work: ...
7
votes
2answers
689 views

Controlling TreePlot (and GraphPlot) layout issue

A continuing battle with Mathematica involves graphics heavy with text labels. For example, the following expression renders so that the "Lifecycle properties..." ...
7
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3answers
290 views

Different colors for nodes in tree plot

I have some list of numbers which I am plotting using TreePlot. This is the code: ...
7
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2answers
346 views

Efficient setting of properties of multiple vertices in Graph

The functions SetProperty and PropertyValue can only set a single property of a single vertex, as far as I know. How do I set a ...
7
votes
2answers
475 views

Can I put tooltips in a Graph?

This doesn't work: Is there a way to do this? My real goal is to identify the second links in the graph below, which shows the results of a webcrawl (using this code). I'm open to another ...
7
votes
2answers
283 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 ...
7
votes
2answers
2k views

How to find the Shortest Path, visiting ALL vertices, without coming back to the start (Hamiltonian Path, minimum distance)

A car has to pick up each person and take them to their destination. I am trying to find the shortest tour that will do this. How can I find the shortest path between any s and t.... visiting all ...
7
votes
4answers
3k views

How to generate and draw simple bipartite graphs?

A bipartite graph is a graph whose vertices can be divided into two disjoint sets. Given two lists: {1, 2, 3} and {x, y, z}, ...
7
votes
2answers
523 views

Edge problems in a directed graph

I want to create the following two graphs. So far I tried the following Code ...
7
votes
2answers
768 views

Coloring edges in GraphPlot

I'm a little stuck with graph drawing part of my research — I can't use the Graph function for plotting my graphs, because my graph is a multi-graph. ...
7
votes
1answer
180 views

Fractal dimension of a large networked molecular system

I am trying to determine the fractal dimension of this complex biomolecule (figure attached). Any clues as to how this can be done. In trying to determine this quantity, I wonder how its ...
7
votes
3answers
317 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
7
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1answer
1k views

Mathematica: Label specific vertices in GraphPlot

How can I label particular vertices in GraphPlot? And have the arrows space out accordingly, for the width of the label? I have Mathematica 7, but I think this question applies to all versions. ...
7
votes
2answers
112 views

How can I recover a graph from a graphical output in a notebook after resetting the kernel?

I have an old Mathematica notebook with an output for a graph structure $G$ I would like to recover. However, the routine for building up the graph is stochastic, so I can't simply rerun the code. ...
7
votes
1answer
342 views

How to implement hive plot for graphs in Mathematica?

I'm trying to implement a version of the hive plot advocated in [Kryzywinski, et al., 2012]. There are many examples of such graphs on the author's webpage. It would be good enough for me to have ...
7
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2answers
874 views
7
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1answer
137 views

Relaxation of Mass-Spring System with Pinned Masses

Problem Assume that four masses are connected to each other by springs while two of them are pinned down at their initial positions. Find the position of masses when system is at its minimum ...
7
votes
1answer
402 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 ...
7
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2answers
208 views

Graph does not accept Property Options

My question is concerned with the Graph functionality, which was newly implemented in Mathematica 8. I already used GraphPlot ...
7
votes
1answer
244 views

How to scale edge length and keep layout of edge-weighted Graph?

I love using Graph as structure to store and visualize my data in Mathematica. Consider the following simple example for creating a ...
7
votes
1answer
196 views

How to set the Y coordinates for a Graph with defined X coordinates to prevent overlap of nodes?

I would like to draw a Graph with defined $x$ coordinates and variable node sizes. If I simply replace the $x$ coordinates of a graph, then nodes can overlap and ...
7
votes
1answer
1k views

Dynamic Graph visualization

I'm working on a C++ library that will be used to construct and study certain graphs (as in a set of connected vertices, not a function plot). These graphs will be dynamic in nature (and can ...
7
votes
1answer
312 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: ...