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

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1answer
64 views

Vertices overlap with vertex labels

How to prevent a behavior on a picture below? Why vertices overlap with vertex labels? ...
0
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1answer
47 views

How to change vertex font size in TreeGraph?

I tried to change vertex label font size by the following code ...
4
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1answer
82 views

How do I change one edge in a tree graph to a double arrow?

I use the following code plot a binary tree and wants to change an edge to double arrow. ...
2
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1answer
218 views

Draw a de Bruijn graph with random vertex size

I am trying to draw a graph that looks like below, This the code I have so far, ...
11
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2answers
125 views

EdgeAdd function not adding edges to a RandomGraph[ ]

Bug introduced in 9.0 or earlier and persisting through 10.3.1 I have a graph: g = RandomGraph[{1, 0}] So basically, it is just one vertex. I want to add some ...
3
votes
1answer
86 views

Deleting isomorphic graphs efficiently

I'm trying to delete isomorphic graphs from a large list. My solution is as follows: DeleteIsoG1[gl_List]:= Module[{}, DeleteDuplicates[gl,IsomorphicGraphQ]]; ...
0
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1answer
70 views

Getting error from CommunityGraphPlot

Situation I'd like analyse my web site with CommunityGraphPlot as follows: Step 1: Define a function to scrape the all the webpages from expected website. ...
2
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1answer
58 views

Deleting Isolated subgraph in a graph

Suppose I have a graph GraphPlot[{1 -> 2, 2 -> 1, 3 -> 1, 3 -> 2, 4 -> 1, 4 -> 2, 4 -> 4, 5->6}] Now I want to identify the vertices of a subgraph which are isolated from the main graph.(In this case ...
3
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1answer
71 views

Cannot get Mathematica to recognise Vertex Weights of Graph

I am using Mathematica Version 8.0 I've tried variations of the following commands, in order to assign the weight $1/k$ for vertex $k$, for a graph defined on {1,2,..,n} via the edge rule $$(k,k') ...
3
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1answer
76 views

Generate all directed graphs with n vertices, + additional constrains

I have a problem similar to Using GraphData to generate all directed graphs with n vertices. That is, I want to have all directed graphs with n vertices (particularly, for n = 4). However: not up ...
9
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0answers
93 views

Set new edge capacity

Bug introduced in 9.0 or earlier and persisting through 10.3.1 I am trying to add a new edge to an existing graph and set its capacity, but for some reason the ...
2
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3answers
90 views

network visualization with different colors for different edge labeled

I have a network with 3 different edge types, edgelist file is a three column file with id1, id2 and edge label. I uploaded the file here What I need know is to find a way to plot this network, as ...
4
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2answers
105 views

How to plot a graph with some disconnected vertices?

I am trying to plot a graph with $6$ vertices but I do not want some of the vertices to be connected. I have drawn a picture to illustrate my problem. So far I know how to plot $6$ vertices without ...
3
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2answers
136 views

How do I find all cut vertices (aka articulation points) in a graph?

Given a connected graph $G = (V,E)$, we say that a vertex $v \in V$ is a cut vertex of $G$ if the removal of $v$ from $G$ causes $G$ to become disconnected. How can I find all cut vertices of a given ...
1
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1answer
53 views

what causes this display problem (missing arrows) with this adjacency graph [duplicate]

AdjacencyGraph[{{1, 1, 0}, {0, 0, 1}, {0, 0, 1}}, DirectedEdges -> True] If you look very closely at the resulting visual display in a notebook (below), you ...
8
votes
1answer
94 views

Smallest connected subgraph containing all given vertices

Given a connected graph $G$ and a subset of its vertices, $S$, I need to find the smallest connected subgraph of $G$ containing all of $S$. How would you approach this in Mathematica? I am asking ...
3
votes
2answers
62 views

Spatial Display of “Union of Geodesics” in a Random Geometric Graph

After reading.... Finding all shortest paths between two vertices which addresses an important topic in Mathematica graph visualisation, I use ...
1
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0answers
55 views

Visualizing site map using a Tree

I've been trying to visualize a sitemap for analysis purposes. So far, using Leonid Shifrin's makeTreeRojo function, I've been able to build a somehow decent visualization. First, I fetch and format ...
5
votes
1answer
173 views

Finding a complete subgraph efficiently

I'm working on some experimental algorithms which would benefit from methods to find an instance of complete subgraphs with N vertices in an undirected graph. This far I've tried these methods: ...
1
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2answers
210 views

Chromatic number for “great circle” graph

I would like to calculate the chromatic number for a great circle graph. I tried this example in this link. I first tried to calculate the chromatic number for ...
2
votes
1answer
63 views

Changing edge weights in a graph using PropertyValue

I encountered a problem trying to change the EdgeWeights in a graph. I am runnning Mathematica 10.1 under Windows 7 Enterprise. I have an undirected graph with 144 nodes and 576 edges. I first ...
1
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0answers
42 views

Depth limited search in mathematica

I often use FindPath[G, 1, 2, {L}, All] where $G$ is some graph. This finds all paths of length exactly $L$ edges which run between nodes $1$ and $2$. In large ...
1
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0answers
79 views

Mathematica in Action (Wagon) — code to generate a great circle is giving error [closed]

I have code from Stan Wagon's Mathematica in Action, Chapter 17 (Great Circle Problem), but when I try to run it, it does not work. I have Mathematica 10. The code that does not run is shown below. Do ...
10
votes
3answers
255 views

Custom edge style (e.g. brush stroke, writing ink, etc.)

I would like to draw a graph with Mathematica in such a way that it looks like a handmade drawing or painting. To be more precise, is there a way to set a custom edge style such that it looks made ...
1
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0answers
50 views

How to set distance between connected vertices in graph?

I'm new at making graphs in mathematica 9, so I don't know if this question is contained in some of already asked ones. I started making it to visualize a polytope, which is build by a sertain ...
3
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0answers
58 views

How best to use or to emulate the “obsolete” Combinatorica command Contract?

The obsolete Combinatorica package has a command Contract for contracting an edge in a graph. Below is my very clunky attempt to work with up-to-date graph objects ...
3
votes
1answer
52 views

TreePlot: arrows on specific lines

I have the following list of rules: L={1->2,2->3,3->3}; and I want to plot a tree graph: ...
1
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1answer
31 views

WeaklyConnectedGraphQ evaluates to False. Is this the expected result?

Take the simple graph {1->2, 2->3, 3->1}: TreePlot[{1->2,2->3,3->1}] I would expect that ...
11
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2answers
248 views

Vertex descendants subgraph

Keywords: vertex, ancestors, descendants, subgraph, directed graph, flow subtree So let's say we have a TreeGraph: ...
1
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1answer
34 views

Scan appears to work setting graph properties, but get error on property-read

This is a self-contained version of something a bit bigger - going for brevity. It is a bit synthetic, but there are applications I have in mind where the {{1,2}} will be replaced with real data, more ...
2
votes
1answer
49 views

Path with no dependence violations

I am guessing this will be a duplicate(it seems like a common task), but I obviously can't find the right page. I have a directed graph showing dependencies, and I want to list the vertices in an ...
5
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0answers
78 views
2
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2answers
149 views

How to find all possible paths with as many edges between two same vertices?

Suppose I have an undirected graph G = Graph[{1 <-> 2, 2 <-> 3, 2 <-> 3, 3 <-> 4}] I used ...
6
votes
2answers
215 views

Extract bibliography from a PDF document

I am trying to extract bibliographies from academic papers which are in pdf format, and I have to do this for 100+ papers. My goal is to create a network of citations amongst the authors and identify ...
6
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2answers
162 views

Grouping the list of numbers that have common.

I am working on some simple problem. It is like puzzle.. Let's say I have some list input={{1,1},{1,2},{1,3},{2,3},{3,3},{4,4}} Which means 1 can go and back to ...
4
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2answers
189 views

Ploting a parallel graph for an animation

I am sorry that my attempt to obtain a fully functional plot as I want failed badly because I am not able to integrate the features to the graph. Here is my simple code: ...
8
votes
1answer
76 views

Is there an easy way to set or retrieve a graph edge properties as a list, in a single go?

I am trying to use arbitrary edge properties in Graphs, and I am looking for easy ways to work with them. In many cases it would be convenient to be able to set ...
0
votes
1answer
69 views

Creating confidence interval plots for random graphs

I have the following code where I create instances of random graphs and use their properties to compute the mean of a quantity labeled 'PoA'. In the last line, I use a range of values for the ...
4
votes
1answer
82 views

How to use the “EdgeLayout” suboption of GraphLayout?

According to the documentation, GraphLayout has an EdgeBundling suboption, which can take the following values: ...
1
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0answers
52 views

Graph equivalent of GraphPlot's MultiEdge style?

I like the default display of Graph much better than that of GraphPlot, but I do not see how to turn off the use of multi-edges ...
8
votes
3answers
244 views

How to count all cliques (not just maximal ones) in graphs?

How can I count the numbers of $r$-cliques in a graph? In other words, the number of triangles, the number of $K_4$, the number of $K_5$ etc. I have tried for example ...
4
votes
1answer
152 views

Fast way to get edge-list of graph in terms of vertex indices (not vertex names)

I am looking for the fastest way to achieve the following: Given a Graph, retrieve its edge list in terms of vertex indices (not actual vertices). For example, ...
1
vote
1answer
67 views

LayeredGraphPlot how to change color of vertex box

For LayeredGraphPlot how to change the default yellow color? ...
2
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0answers
81 views

How do I get all possible paths in terms of edges, and not vertices in Mathematica?

Suppose I have an undirected graph ...
0
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3answers
109 views

How to Change Vertex List in a Grid Graph

I would like to actually change the vertices in a grid graph instead of simply changing the label. Ultimately, I want the vertices to be points on a plane. So if given a simple grid graph ...
2
votes
1answer
58 views

How to draw vertices with identical names multiple times?

I have a list of rules that I would like to show as a layered graph. However, some vertex names appear more than once. How would one best deal with this situation? Example: ...
4
votes
1answer
86 views

Is there a way to efficiently generate a large “incomplete” k-partite graphs

A complete k-Partite graph can be divided into "k" distinct sets of nodes, each of which is connected to all nodes not in its own set. This can be generated with code CompleteGraph[{an, bn, cn}] ...
5
votes
0answers
129 views

Number of 4-colorings of Johnson solids

I want to know the number of 4-colorings for all Johnson solids. This is equivalent to evaluating the flow polynomial for the corresponding polyhedral graphs at $k=4$. I tried the following to get ...
0
votes
3answers
98 views

Weighted and directed network computation in Mathematica

Is there any set of commands in Mathematica to compute mean shortest path, global clustering coefficient, diameter and radius of the network, etc. for weighted and/or directed graphs? There indeed ...
11
votes
1answer
136 views

How can I route edges manually for a Graph?

Most graph layouts supported by Mathematica use straight lines for edges; or at least something that only depends on the coordinates of the two adjacent vertices of the edge and nothing else. A ...