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

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3
votes
1answer
112 views

Expected graph distance in random graph

I am trying to use the functionality of Expectation and Probability for random graphs, in particular for percolation models. ...
3
votes
2answers
206 views

Positioning Vertices in a Graph

I made a graph that has a given number at each vertex: I want to place vertex 1 above vertex 2 if value of vertex 1 is larger than of vertex 2. And also, vertices with same value should be located ...
1
vote
1answer
264 views

Vertex labels versus vertex names in VertexRenderingFunction

The VertexRenderingFunction seems to only use names, not labels. For example: ...
2
votes
1answer
187 views

Plotting attributes of vertices in WattsStrogatzGraphDistribution[n, p, k]

I have a graph WS = RandomGraph[WattsStrogatzGraphDistribution[n, p, k]]. I need to plot several characteristics of each v: the ...
2
votes
1answer
147 views

Want to label vertices of a graph and manually move them around

I would like to plot a graph in such a way that The vertices are labeled using labels that I've given them, rather than just their number, I can manually move the vertices around. In the code ...
0
votes
2answers
216 views

Plot “number of triples at each v in V(G)” [closed]

For a uni assignment, I need to plot the "number of triples at each v in V(G)". I tried to find relevant information in the Mathematica documentation through Google, but I'm lost. How do I get the set ...
2
votes
1answer
76 views

Fix the size of vertices and arrow in graphs

I defined an option to draw nicely the graph. But I have a problem with the different size obtained. For example, the layout of the first graph is what I want to have for all other graphs I will ...
3
votes
2answers
182 views

How to get all leaves from a graph's specific node

Let's say I have this graph (The code to generate the graph is at the end) How can I extract all the leaves comming from, let's say "cluster3"?, i.e. {100, 92, 87, 89} I guess I have to first ...
5
votes
1answer
255 views

Implementing local complements of graphs

I'm trying to write a routine which generates the local complement of a graph at a vertex. For those who don't know, the local complement for a singly-connected, undirected graph is defined as the ...
1
vote
0answers
52 views

Graph plotting: specify layers for layered drawing

Mathematica can do layered graph drawing with LayeredGraphPlot or GraphLayout -> "LayeredEmbedding". Is it possible to ...
3
votes
0answers
147 views

Undirected Network and its Monte Carlo Simulation

So I have this array of points, in the form {x, {y,z}}, where x is the node number assigned when I used the locator pane to make a network, and y and z are its unitary coordinates. The graph is made ...
4
votes
1answer
136 views

Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
3
votes
1answer
156 views

Cellular Automata Neighborhood as Node connections

Can I use the CellularAutomation[] function where the neighborhood is defined by the connections between nodes? For example, if 1 -> 2, 1 -> 3, 1 -> 8, 1 ->1, then the neighborhood of node 1 is the ...
3
votes
0answers
51 views

Does anyone know the options for “HierarchicalEdgeBundling” in Mathematica?

I'm looking to reproduce the types of graph layout that are possible in D3 (http://bl.ocks.org/mbostock/7607999) in Mathematica. Since Mathematica doesn't explicitly support force directed edge ...
3
votes
2answers
157 views

Harmonious graph labeling

Is it possible to harmoniously label a graph in Mathematica? I would like a function, that when given a graph, would return a harmonious labeling. If not, is there other software that can do it? A ...
2
votes
4answers
310 views

How to plot a graph from it's incidence matrix?

I'm using Mathematica v9 and am trying to draw a graph by using it's incidence graph, but it won't draw it, which occurs an error "is not a valid incidence matrix.". But I've checked my matrix, and ...
6
votes
2answers
301 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 ...
4
votes
1answer
102 views
2
votes
2answers
261 views

Manipulate graphs in 3D

Is it possible to Manipulate Graphs (e.g. a ...
19
votes
5answers
1k views

How can I replace bi-directional DirectedEdge pairs in a Graph with a single UndirectedEdge?

The Cayley graphs produced by Mathematica 8.0's CayleyGraph function represent actions that are their own inverses in an unconventional way: rather than using a ...
13
votes
4answers
13k views

Finding all simple paths between two vertices in a graph

There are built-in methods to find a shortest path between two vertices in a graph, and the question on finding all shortest paths between two vertices has gathered quite a bit of attention. A path ...
2
votes
3answers
300 views

How to draw a combinatorial graph with different colors of edges?

For example, like above. I've read some examples and descriptions in here, but couldn't figured it out.
3
votes
1answer
57 views

Make AdjacencyGraph hide single unconnected elements

Is there a way to force AdjacencyGraph to hide single unconnected or self connected elements? ...
9
votes
1answer
269 views

Dual graph of an arbitrary (planar) graph

Every planar graph has a dual. How can I obtain it with Mathematica? I know that GraphData provides the DualGraph property for ...
5
votes
3answers
200 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 ...
0
votes
1answer
181 views

Creating a Network from a Output

So I used the locator pane to derive the positions of a vertex on a picture. The picture was the Maryland Power Grid and the vertices were the generators and loads of the power system. When I clicked ...
1
vote
2answers
96 views

How can I speed up the export of graphs in DIMACS format?

I'm creating random graphs with suitable properties and exporting them in the DIMACS format. Already, for rather small graphs with, say, ~60k vertices and ~240k edges, ...
14
votes
4answers
512 views

Can TreeForm be displayed “sideways”?

One recurrent problem I'm having with displays generated with TreeForm is that the expressions to be so displayed often at least one level with many (> 20) nodes ...
30
votes
8answers
2k views

Longest path in 0/1 matrix

I have a matrix of 0's and 1's forming a number of disjoint paths:   I would like to find the lengths of the paths, and from that "spectrum," the longest length (in the above example: 27, ...
4
votes
2answers
127 views

How to obtain all the distinct De Bruijn sequences?

In combinatorial mathematics, a $k$-ary De Bruijn sequence $B(k, n)$ of order $n$ is a cyclic sequence of a given alphabet $A$ with size $k$ for which every possible subsequence of length $n$ in $A$ ...
6
votes
2answers
146 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 ...
7
votes
3answers
305 views

Nested list to graph

The following nested list can be regarded as a representation of a (tree) graph: ...
4
votes
1answer
119 views

The algorithm of ListGraphs[n,m]

I'm not sure if this is a Mathematica problem, math problem or a CS problem, so if this is off-topic please transfer it. In the package Combinatorica there is a ...
3
votes
2answers
126 views

Vertex Names of Subgraph in Order of Connectivity

I extract path subgraphs $P_4$ of an undirected graph $G$. And want to list the VertexNames of the subgraphs in the same order as they are connected. Here is an example: ...
0
votes
0answers
34 views

Find set of subgraphs of g1 isomorphic to g2 [duplicate]

I would like to find all the subgraphs of a given graph g that are isomorphic to the graph h. My current code doesn't work how it should. Many solutions are missed and I think something is ...
2
votes
3answers
170 views

Sequence of binary trees with different source nodes and with the same Strahler hierarchical order

I would like to create a picture which contains a sequence of binary trees with the same Strahler hierarchical order (for example equal to 2) e with a sequence of different source nodes "i" (from 1 to ...
0
votes
0answers
56 views

how to rewire the minimum number of edges in a disconnected bipartite graph, so to transform it in a connected one

Consider an incidence matrix A for a bipartite graph (Aij=1 if node i of group 1 and node j of group 2 are connected). A is not symmetric. Assume that A is disconnected or only weakly connected, i.e. ...
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}, ...
1
vote
1answer
89 views

Rendering of a HighlightGraph in a Manipulate content pane distorted by changing the highlighted edge

A HighlightGraph inside a Manipulate initially displays correct however after approximately 2 seconds, the layout changes and ...
3
votes
2answers
128 views

Labeling vertices by number in Graph: Getting text to display at the right size

Minor aesthetic question here. I was playing around with Graph's and decided to render a cute-looking family of directed graphs, with the vertices being the number ...
3
votes
0answers
187 views

Understanding performance: graph connected components

I need to analyze directed graphs with 10M edges, 1M vertices, and 300K strongly connected components, so that the largest one contains 400K vertices. I read some explanations of Leonid Shifrin here, ...
1
vote
2answers
80 views

Using Combinatorica`ListNecklaces in v9

I am using Mathematica for visualization of DeBruijn graphs. However, I am having a bit of trouble using ListNecklaces. I want to know how many cyclic shifts of ...
2
votes
1answer
131 views

distance between each vertex of a graph and its output

I have a question regarding this Q&A. Let's call a vertex that is not the tail of any directed edge an output of the graph. The graph below has only one output (at the far right). If I want the ...
17
votes
5answers
614 views

Graph from binary matrix (not adjacency) respecting the original matrix positions

I have a binary matrix. My objective is to connect every close (without "jump") elements with value equal to 1, but I must keep the point positions, just like it's shown at the image. Can somebody ...
0
votes
0answers
99 views

Centrality measures and normalisation

Are centrality measures normalised in Mathematica 9? Only ClosenessCentrality is normalised. How I can normalise other centrality measures notably ...
8
votes
2answers
357 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 ...
1
vote
0answers
212 views

Triangular lattice with periodic boundary conditions

I am trying to generate an equilateral triangular lattice with fixed vertices and periodic boundary conditions. I am supposed to assign an index (starting from 0) to each vertex in my lattice and then ...