Questions about handling graphs in Mathematica, graph theory, graph visualization, GraphPlot, the built-in Graph type and the Combinatorica` package.
4
votes
2answers
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 ...
3
votes
1answer
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,
...
13
votes
3answers
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 ...
4
votes
1answer
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 ...
4
votes
1answer
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.)
...
10
votes
2answers
232 views
Proper way to add vertices to an adjacency matrix
I'm looking for a robust way to add vertices to a graph by modifying its AdjacencyMatrix.
Here's what I have so far:
...
5
votes
3answers
138 views
StandardForm on Graph edges
The Graph command displays edge labels in TraditionalForm. I instead want to use ...
16
votes
3answers
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 ...
11
votes
2answers
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 ...
6
votes
4answers
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 ...
13
votes
3answers
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 ...
4
votes
1answer
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: ...
12
votes
3answers
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 ...
12
votes
2answers
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:
...
2
votes
1answer
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:
...
1
vote
1answer
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 ...
2
votes
2answers
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 ...
3
votes
2answers
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?
...
4
votes
1answer
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 ...
18
votes
2answers
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 ...
4
votes
1answer
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 ...
6
votes
2answers
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:
...
15
votes
1answer
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 ...
13
votes
3answers
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
...
12
votes
2answers
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 ...
14
votes
2answers
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 ...
6
votes
3answers
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 ...
16
votes
3answers
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 ...
8
votes
2answers
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 ...
2
votes
2answers
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:
...
2
votes
0answers
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:
...
14
votes
1answer
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 ...
7
votes
2answers
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..." ...
10
votes
2answers
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 ...
4
votes
0answers
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 ...
14
votes
1answer
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 ...
14
votes
1answer
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?
1
vote
0answers
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 ...
10
votes
2answers
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 ...
6
votes
1answer
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, ...
11
votes
1answer
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
...
5
votes
3answers
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:
...
6
votes
2answers
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 ...
8
votes
2answers
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?
...
6
votes
2answers
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 ...
6
votes
1answer
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 ...
7
votes
2answers
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:
...
4
votes
1answer
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 ...
6
votes
2answers
169 views
Visualize the output of Trace in a tree structure
The output of Trace[expr] can be nicely represented as a tree, I guess.
Here is an example trace.
...
3
votes
3answers
459 views
How to draw a directed graph with arrows showing vertically from bottom to top
If I have a directed graph, how can I draw it with arrows pointing vertically from bottom to top, like showing a class inheritance pattern in OOP(object oriented programming)?
