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

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7
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2answers
544 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
1answer
156 views

Replacing graph nodes with matrices

I would like to label a graph with matrices. Suppose the graph is simple: And I have an array mats that contains the labels for vertices 1,2,3,4 (these are just random 0-1 matrices; ignore the ...
7
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1answer
321 views

Coloring edges of a graph according to their weight?

What's the simplest way to plot a graph with weighted edges, such that the color of the edge corresponds to the weight of the edge?
7
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2answers
378 views

Colorize and the Four-Color Theorem

We can write: MorphologicalComponents[image] // Colorize To assign a random set of colors to each component in some image. The example used for reference by ...
7
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2answers
553 views

Edge problems in a directed graph

I want to create the following two graphs. So far I tried the following Code ...
7
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2answers
847 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
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4answers
270 views

Automatically convert pairs of directed edges to an undirected edge?

I have a directed graph, which for some pairs of vertices, has a directed edge between them in each direction. I would like to replace such pairs of directed edges between the same vertices but in ...
7
votes
1answer
201 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
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3answers
362 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
7
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2answers
589 views

How to add new nodes to an existing graph with fixed (coordinates) nodes?

I'm ultimately trying to create a directed graph with some of the nodes in fixed positions and the other nodes placed around them in "acceptable" positions. It's better if I ask the question by ...
7
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1answer
308 views

What algorithm is Mathematica 9 using for “SpectralEmbedding” of graphs?

When I specify that a graph should be realized using the "SpectralEmbedding" procedure, what paper / algorithm for spectral embedding is this based on? I was unable to find any documentation for ...
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
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2answers
116 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
288 views

How to view all graphs available in GraphData?

Is there a "gallery" view of all the graphs available in GraphData? I realize that some graphs may not lend themselves to such representation (e.g. some may have ...
7
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1answer
364 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
votes
1answer
373 views

How to determine edgeweights from width of skeleton using MorphologicalGraph (or workaround)?

Background I'm trying to create a workaround for what seems to be a bug in MMA's graph functions related to edge weights: SO: How to Label Graph Edges with their weights According to MMA's ...
7
votes
1answer
431 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
210 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
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1answer
97 views

Setting PropertyValue for VertexWeight is not persistent

Bug introduced in 9.0.2 or earlier and fixed in 10.0 ...
7
votes
1answer
273 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
208 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
342 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: ...
7
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1answer
461 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 ...
7
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0answers
191 views

How to generate a random flow graph?

A flow graph is a rooted directed graph that the root reaches all other vertices. I need to generate a random flow graph in Mathematica. My idea is to use ...
7
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0answers
43 views

What system functions use VertexWeights?

EdgeWeights -> are used by a lot of functions, but I can't find any exposed usage for VertexWeights ->. I'm not asking ...
7
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0answers
278 views

How to draw hypercube graphs

I'd like to draw hypercube projections like those on the Wikipedia page: I tried with HypercubeGraph[6] but the graph does not look right; it is not ...
7
votes
1answer
255 views

Making FindShortestPath a little bit sloppy [duplicate]

I have a dense graph, and I'd like to find multiple "almost shortest" paths from a source vertex, $v_s$, to a sink vertex, $v_s$, on an undirected graph $G$. How can I repeatedly run ...
6
votes
4answers
227 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 ...
6
votes
2answers
144 views

Visualizing subgraphs while specifying the locations of vertexes

I would like to visualize separate connected components of a graph defined by data points lying in the two-dimensional plane by surrounding each connected component subgraph by a bounding curve. I ...
6
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2answers
409 views

Don't understand why Mathematica is complaining about my Graph expression; how can I fix it?

The Tube in Arrow problem is fixed in version 10. Note that in version 10 Graph3D must be ...
6
votes
4answers
3k views

How to generate random directed connected graph?

How to generate random directed connected graph? I need to create graph which will pass: ConnectedGraphQ[^]
6
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2answers
2k views

Eigenvalue / Eigenvector Calculation

I'm currently trying to compute the three smallest eigenvectors for a 34 by 34 matrix. While I was expecting this to take some time, Mathematica has been running for the past 3 hours, which seems ...
6
votes
2answers
243 views

How to make each node of a graph a button?

A newbie question this one - MMA help seems to suggest it would be possible to place a button on ( or have a button be ) each node of graph, labelled with the name of said node. I have no idea where ...
6
votes
3answers
818 views

Graph adjacency matrix with unconnected nodes

I am trying to display a series of 9x9 adjacency matrices which represent directed graphs on a 3x3 grid. The issue I am running up against is this (compounded by that fact that I don't really know how ...
6
votes
3answers
229 views

Converting expressions to “edges” for use in TreePlot, Graph

This question is similar to this: Nested list to graph. How to "flatten" an arbitrary expression, eg expr = a[b[c, d[e][f], g], h] to a list of key-value pairs ...
6
votes
3answers
394 views

Flow in pipeline graph

I have pipeline directed graph which has one source and several sinks ...
6
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3answers
215 views

Drawing a graph with vertex avoiding edges? (Handling vertices that must be colinear?)

I'd like to draw something like the following graph: ...
6
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2answers
162 views

Why the Mouse dragging response not as smooth as Locator

I am experimenting to use MouseDragged eventhandler to change the vertices positions of a triangle, it works, but not as smooth as using Locators. Is this the ...
6
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3answers
177 views
6
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3answers
536 views

How to extract edgeweights from a graph

I have a graph with weighted edges, and I'd like to obtain the edge weights of the edges in the graph. Is there a nicer way of doing this than getting the ...
6
votes
2answers
78 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. ...
6
votes
2answers
335 views

How to color edges of a graph which has multiple edges connecting certain vertices

I'm studying BIBD(Balanced Incomplete Block Design) and want to draw some graphs by coloring their blocks in different colors, respectively. A block is a collection of edges (or vertices). For ...
6
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1answer
690 views

How to turn a random graph into a matrix

I have constructed a random graph with Mathematica using the RandomGraph command. Now I would like to convert this graph to a matrix, but I don't know how. The ...
6
votes
1answer
600 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 ...
6
votes
1answer
809 views

How can I draw a polygon from a set of angles?

In recreational mathematics, polytans are polygons formed by edge-connecting isosceles right triangles. Order-n polytans are those constructed from n such triangles. My question is this: Given a ...
6
votes
2answers
275 views

Truncate TreeForm to show only the top

For some expressions, TreeForm may grow very long. I'm only interested in the top levels of the expression. How can I get the tree form of only the first levels an ...
6
votes
1answer
92 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. ...
6
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3answers
315 views
6
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3answers
273 views

Enumerate the 1-factors (perfect matchings) of $K_n$

Introduction I would like to enumerate the 1-factors, or (near-)perfect matchings, of the complete graph Kn. The adjacency list representation for Kn is basically { (x, y) | 1 ≤ x < y ≤ n }. For ...