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

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9
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1answer
326 views

Caching of Graph Graphics

In this answer, Simon Woods concludes that when you display an expression with head graph more than once, something is getting stored somewhere. I looked into it too and found out this only happens if ...
7
votes
2answers
395 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 ...
4
votes
2answers
134 views

BezierCurve in EdgeShapeFunction fails when used on multiedges graph

I would like to create a network graph with curved edges. To do this, I wrote this function: ...
4
votes
1answer
199 views

How to set FindGraphCommunities Modularity's method option

It is possible to set 2 options for one of FindGraphCommunities's methods "Modularity". They are "Weighted" and "StopTest". The question is how can one use the second option "StopTest"? What ...
4
votes
1answer
2k 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: ...
1
vote
1answer
614 views

Adding an image background to a graph that uses vertexposition

Hello Mathematica stackexchange community! I need your help on a research project. I'm looking to create a graph g with vertices in specifies places and then use an image I have as the background of ...
1
vote
1answer
152 views

How can I change the Graph required data such as EdgeWeight,VertexWeight,EdgeCapacity,VertexCapacity in the Graph?

I asked this question in different form and because I couldn't receive the proper answer so I have to change my question.I know that was my fault sorry.I need to change the Matrix Data of nodes and ...
10
votes
4answers
651 views

Ordering vertices in GraphPlot

I'm new here, so forgive me if this question is not well-posed/duplicates an earlier question - although I've searched for similar questions without success. I'm trying to present a plot of ...
7
votes
2answers
494 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: ...
7
votes
2answers
707 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. ...
6
votes
3answers
684 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 ...
5
votes
0answers
154 views

Citation of the algorithms used in FindGraphCommunities

For my research work I need to put a comparison of different community detection algorithms. Instead of implementing all those algorithms once again, I would like to use the methods already provided ...
3
votes
1answer
96 views

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

I'd like to draw something like the following graph: ...
0
votes
1answer
136 views

How to implement the directed Barabasi-Albert algorithm in Mathematica?

Does anyone know how to implement an efficient version of the [directed Barabasi-Albert algorithm][1] in Mathematica that scales until hundred of thousands nodes? The directed network mechanism is ...
25
votes
4answers
3k views

How to generate a random tree?

Is it possible to generate a random tree without explicitly constructing a random adjacency matrix that satisfies tree properties? How about a random directed tree? Edit: incredible answer by ...
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, ...
17
votes
3answers
1k 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 ...
16
votes
2answers
708 views

How to measure segment length and branch angle

I am trying to measure segment length and branch angle or bifurcation angle between each pair of segments. My image after thinning looks like this: ...
19
votes
1answer
451 views

How to visualize large graphs with directed edge bundling

I'm wondering if anyone has implemented edge bundled graph plotting? http://www.win.tue.nl/~dholten/papers/forcebundles_eurovis.pdf
16
votes
4answers
702 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 ...
14
votes
2answers
615 views

How can I speed up the classic GA for graph coloring?

I'm trying to compute the chromatic number of this graph (which is 28): g = Import@"http://www.info.univ-angers.fr/pub/porumbel/graphs/dsjc250.5.col"; My genetic ...
12
votes
2answers
1k 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 ...
11
votes
2answers
189 views

Graph smoothing keeping vertices fixed?

Context Given a Graph like this one: ...
11
votes
1answer
351 views

Dynamic visualization of Graph[] on a webpage

How can we embed a dynamic version of a Graph object on a web page, similar to the one showcased on the networkx home page? This sort of dynamic visualization can ...
10
votes
1answer
654 views

Roads network visualization by thickness and color intensity by population from GIS files

We can have road networks of the countries in GIS shape file.For exmple from here. Normally traffic flows are proportionate to populations of the cities. I wonder how we can have the same in ...
16
votes
3answers
473 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 ...
12
votes
2answers
514 views

Calculating morphometric properties

Is it possible to calculate segment length, segment diameter and branch angles for three dimensional geometry. Geometry contains vertex points and polygon surfaces as ...
8
votes
1answer
172 views

Vertex merging in graph?

Given a Graph such as the one produced with the following code ...
6
votes
1answer
300 views

Connect neighbouring points as list of segments in 2 D

Context I am interested in connecting neighboring points in 2/3D as list of segments. I am guessing this is something within the reach of graph theory, which is well implemented in mathematica. ...
20
votes
1answer
937 views

Graph vs GraphPlot

What is the difference (in purpose) between Graph and GraphPlot? Which function is bested suited to which tasks? Background: I ...
15
votes
3answers
255 views

What is the most convenient way to change options for Graph[] objects?

What is the most convenient way to change options such as VertexLabels in existing Graph objects? (Version 7 users note: ...
8
votes
4answers
323 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 ...
7
votes
1answer
389 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 ...
19
votes
2answers
386 views

Packed Graph or GraphPlot output with non-square layout?

Graph or GraphPlot produce square layouts for disconnected graphs: Graph[Table[i -> Mod[i^3, 100], {i, 1, 100}]] I´d like to get a rectangular layout with ...
13
votes
4answers
465 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 ...
11
votes
2answers
527 views

Dynamic graphics are less responsive inside a Manipulate

I have some code which displays a GraphPlot and allows the user to click on any vertex in the graph to display some information about that vertex in a popup window. ...
9
votes
2answers
542 views

Extracting vertex coordinates from an automatically laid out graph

Given a Graph with an automatically computed layout (i.e. not explicitly given VertexCoordinates, but using a ...
9
votes
2answers
321 views

Transition between graphs

I want to visually demonstrate the manipulations made to a graph. For instance, I have a graph g where using the command ...
6
votes
5answers
530 views

Building graph based on the cities connection?

I built a Graph based on the permutations of city's connections from : ...
5
votes
3answers
259 views
5
votes
2answers
271 views

Is there something akin to “SubgraphIsomorphismQ” in Mathematica 9?

Provided two unlabeled graphs, $G$ and $H$, I would like to test where $H$ is a subgraph of $G$. In other words, I'd like to test whether we can prune some fixed number of vertices or edges from $G$ ...
1
vote
1answer
243 views

Display a labeled multigraph

Despite the integration of graphs and networks, multigraphs are not supported in Mathematica 8+. In Mathematica 9+, GraphPlot misbehaves for multigraphs having ...
14
votes
1answer
393 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?
12
votes
1answer
200 views

Layout a second graph of the same nodes in the same way

I have a number of graphs with the same nodes. I would like to be able to somehow save the layout that results from the spring embedded results of one graph (the first image), and have the other ...
9
votes
3answers
235 views

Label multiple edges between same vertices

I have a simple graph with multiple edges between two vertices, say: Graph[{ Labeled[a -> b, "A"], Labeled[a -> b, "B"] }] Unfortunately, Mathematica ...
9
votes
3answers
403 views

FindShortestTour for charity (or: How can I optimize meal delivery with FindShortestTour?)

I've been wondering about this for a while - but never got around to asking - until I saw faleichik's incredible answer to Mathematica Minecraft. I did some work at a not-for-profit a little while ...
9
votes
2answers
281 views

Determining whether two $k$-chromatic graphs are isomorphic (respecting vertex coloration)

Consider the case where I have two $k$-chromatic graphs $G_1$ and $G_2$, i.e. two graphs where individual vertices can be colored with one of a set of $k$ total colors, and I would like to determine ...
6
votes
3answers
323 views

Flow in pipeline graph

I have pipeline directed graph which has one source and several sinks ...
6
votes
1answer
243 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 ...
5
votes
1answer
481 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 ...