Tagged Questions

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

121 views

Odd behavior of GridGraph and DirectedEdges

For some reason the option DirectedEdges->True, albeit working internally with grid graph, does not appear in the visualisation for 1D and 2D graphs. It also ...
99 views

Using EdgeList on a once empty Graph crashes the kernel

Calling EdgeList on a non-empty graph which was previously empty causes the math kernel to crash. For example, ...
337 views

Determining all possible traversals of a tree

I have a list: B={423, {{53, {39, 65, 423}}, {66, {67, 81, 423}}, {424, {25, 40, 423}}}}; This list can be visualized as a tree using ...
143 views

Enhancing GraphUtilities' GraphEdit

One thing I use Mathematica for is building molecular graphs. Until now, I've been content with generating an adjacency matrix from SMILES data, and passing that to ...
151 views

How do I find a weighted bipartite graph's minimum edge cover using Mathematica 8?

In graph theory, we use the Hungarian Algorithm to compute a weighted bipartite graph's minimum edge cover (a set of edges that is incident to every vertices, the one with the minimum total weight.) ...
232 views

I'm looking for a robust way to add vertices to a graph by modifying its AdjacencyMatrix. Here's what I have so far: ...
138 views

StandardForm on Graph edges

The Graph command displays edge labels in TraditionalForm. I instead want to use ...
322 views

How to get complete Documentation Center graph of guide pages?

On the very last image below you can see a typical path of walking through Documentation Center guide pages. What is the best way to get the graph data and visualize the whole structure of these ...
690 views

How to convert an image to a graph and get the positions of the edges?

I am trying to convert an image to a graph. My image is already skeletonized and looks pretty much like this: What I need to do is identify all vertices and edges, and in particular get a list of ...
237 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 ...
512 views

Creating diagrams for category theory

Lately I've been doing algebra and I have found myself drawing a bunch of diagrams when I attempt to solve a problem. Most of the diagrams are very simple so I thought, I bet I can do this in ...
367 views

Is it possible to generate a Hasse Diagram for a defined relation?

I'm looking for a way to create a Hasse Diagram from a given partial order binary relation. The relation will be given explicitly, for example: ...
311 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 ...
222 views

Comfortable Edge Labeling of Undirected Graph

I'm working on a program that finds special [called "interval"] edge-colorings for graphs. Output is as follows: ...
122 views

GraphEdit making edges straight

When using a GraphEdit to alter a graph, is there a way to make the edges straight from one vertex to another? Thanks Here is my code: ...
118 views

Recovering vertex names from Combinatorica Graph

According to WRI tech support: Combinatorica functionality is not technically deprecated, though it is our hope that future versions of Mathematica will subsume it entirely by incorporating its ...
116 views

Working around behaviour of EdgeRenderingFunction

One can make graphs GraphPlot[{1 -> 2, 2 -> 3, 3 -> 4, 4 -> 5, 5 -> 1, 1 -> 1, 5 -> 5}] and one can generalize the input such that one ...
85 views

Turning evaluation off

I am making a directed graph, but Mathematica keeps trying to evaluate my labels. I know that I can just use " ", but I have a lot of input. Is there a way to turn evaluation off? ...
173 views

Counting the size of the minimum cut produced by MinCut of GraphUtilities

I want to use the MinCut function of the GraphUtilities package to find minimum cuts for a few graphs. I'm completely new to ...
940 views

Cycles of length N in a graph

If I have an undirected graph represented with an adjacency matrix, how can I find all the subgraphs which are a cycle of length N? I don't really know the math nor the programming language well, so ...
510 views

When do I use Mathematica, when do I use Gephi, and how do I use them together?

Mathematica has great operations for analyzing graphs but when the graphs are a bit bigger, Gephi seems to be more efficient (at least on my computer) at drawing and analyzing, i.e. visualizing the ...
399 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: ...
414 views

How to export and import Graphs with additional data?

I'm trying to export and then later import graphs with additional data added such as VertexLabels and EdgeLabels. When I export ...
396 views

How to find all vertices reachable from a start vertex following directed edges?

How to find all vertices reachable from a given start vertex following directed edges, in a cyclic directed graph given as ...
770 views

Simple algorithm to find cycles in edge list

I have the edge list of an undirected graph which consists of disjoint "cycles" only. Example: {{1, 2}, {2, 3}, {3, 4}, {4, 1}, {5, 6}, {6, 7}, {7, 5}} Each ...
446 views

Graph layout on a grid

Is it possible for Mathematica to layout a graph so that the connections lie on a grid? Furthermore, for graphs with multiple edges per vertex, is it possible to specify the location on the vertex ...
304 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 ...
717 views

Generating graphs interactively (GUI)

I want to create graphs interactively using a GUI. I thought of using a ClickPane[] environment. The code I have (in part borrowed from the Documentation) works ...
159 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 ...
120 views

Is it possible to use PropertyValue to modify properties of Graph objects in a list?

This post can be seen as a follow up to Property assignment on a graph vertex using PropertyValue does not work inside a function. I have defined a function: ...
158 views

How to predict some constant number of values with NeuralNetworks

Example: << NeuralNetworks data = {Sin[#]} & /@ Range[0, 4 Pi, 0.5]; learn = data[[1 ;; 15]]; Now, lets fit our neural network: ...
300 views

Need tips on improving this directed graph

First we define a function that returns the least odd prime factor. lopf[n_] := FactorInteger[n][[2, 1]] Then we craft a routine that performs the 3x+1 steps ...
283 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..." ...
210 views

Using Gather to rearrange my data

I have a list of elements: {{1, 2}, {1, 5}, {2, 6}, {3, 7}, {4, 8}, {5, 6}, {5, 9}, {9, 13}, {10,11}, {11, 12}, {11, 15}, {15, 16}} I have to divide it into ...
159 views

How to compute the genus of a Graph?

What's the simplest way to compute the genus of a graph using Mathematica? I have looked for a Genus function (even in the ...
412 views

Graph vs GraphPlot

What is the difference (in purpose) between Graph and GraphPlot? Which function is bested suited to which tasks? Background: I ...
281 views

When to use built-in Graph/GraphPlot vs. Combinatorica

What are the pros and cons of using built-in Graph/GraphPlot (and related) types vs. types in the Combinatorica package?
121 views

How do I reorder vertices in a graph?

I have a directed acyclic graph $g$, and I'd like to re-order the vertices in this graph object such that when I call VertexList[myGraph] the vertices appear in ...
271 views

Select a directed SubGraph without sinks and sources

Consider the following problem: Assume you have a large list of directed edges, that constitute a large graph. I would like to provide an initial subset of vertices and I need to know which additional ...
124 views

Vertices, their labels, and how to refer to them?

In the examples I have seen, graph vertices in Mathematica are usually explicit small integers. However, Wolfram documentation says that vertices can be any arbitrary expression (eg., george, x^2, ...
179 views

Ulam's Spiral with Opperman's diagonals (quarter-squares)

First we craft a function to return the quadrant boundary based on Oppermann's Conjecture a[n_] := (Mod[n, 2] + n^2 + 2 n)/4 Then we create a few lists ...
149 views

Rendering polygon as graph with directed edges in Mathematica

In Mathematica I'm trying to render a polygon as a set of vertices and directed edges. What I have so far: ...
163 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 ...
217 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? ...
185 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 ...
101 views

Property assignment on a graph vertex using PropertyValue does not work inside a function

I created this function: AddStone[board_Graph, v_, s : white | black | empty] := PropertyValue[{board, v}, VertexState] = s This function should change the ...
240 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: ...
139 views

Removing edge weights from a Graph

How can I remove EdgeWeights from a Graph without affecting any other properties of the graph? Let's construct a graph with ...