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Questions tagged [graph-tool]

Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks).

Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other Python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance which is comparable (both in memory usage and computation time) to that of a pure C/C++ library.

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283 questions
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Filtering a subgraph in graph-tool

This is a ridiculously basic question about graph-tool which should be trivial to figure out how to solve using the documentation, but I'm spinning in circles. I don't doubt that documentation comprehensive, but it certainly isn't making this…
gogurt
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Building graph-tool on OSX with Python 3.4

I tried to install graph-tool on Mac OSX 10.10 using homebrew. The brew build process works fine, but when I try to import graph-tool I get the error described in this question. Another problem with homebrew is that I always builds graph-tool for…
MaxPowers
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Graph tool - Stochastic Block Model vs Leiden

I'm calculating network communities for 4 networks using 2 methods: 'Leiden' method, which gives me 7 (a), 13 (b), 19 (c), 22 (d) communities. 'Stochastic block Model', also checking group membership of the nodes by inspecting levels of the…
8-Bit Borges
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Circular layout with edge bundling and labels in graph-tool

I am very new to graph visualizations and software like graph-tool (gt). My main field is mathematics, but I am somewhat familiar with Python and programming in general. However, I'm not a programmer, so my code may be less than elegant; any…
Christopher.L
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graph-tool Make text fit to the vertex

I am ploting the graph with big labels. Is there a way to wrap the labels so they would fit in the vertex of the size. this is what I have so far p1 = gt.graph_draw(gr1, output_size=(2000, 6000), pos=pos1, …
Saveliy Belkin
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Setting edge length in graph-tool output

I`m looking for the way to specify precise lengths of edges in graph to get appropriate drawing. I`ve tried to make it via edge properties: import numpy as np import graph_tool.all as gt tree = gt.Graph() # ddmatrix is a symmetric adjacency…
Arleg
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python graph_tool: get _all_ shortest paths

I want to compute all shortest paths between all pairs in a graph. To achieve this, I am using graph_tool's all_shortest_paths function for every node pair in the graph. According to the documentation, the function is able to respect edge weights,…
startled_sheep
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python graph-tool access vertex properties

For my current project I want to use the graph-tool library since they claim being the fastest: https://graph-tool.skewed.de/performance. I have some algorithms (shortest path, etc.) to run on really large networks, so the faster the better! First…
JustSomeone
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Activating cairo-dependent features of graph_tool

I have been using the graph-tool library for a while now, thus far I hadn't really been using most of its drawing features. Today when trying to use graph_tool.draw.graph_draw I realised that I had configured graph-tool initially without…
Ellie
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python graph-tool load csv file

I'm loading directed weighted graph from csv file into graph-tool graph in python. The organization of the input csv file is: 1,2,300 2,4,432 3,89,1.24 ... Where the fist two entries of a line identify source and target of an edge and the third…
Nidjsi
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Weighted Degree Distribution in Python's graph_tool

In Pythons graph_tool, is there an easy way to calculate the weighted degree distribution (sum of the weights on out-going, in-coming, or all edges)? In the Stats package, vertex_hist gives the un-weighted in-degree, out-degree, and total-degree…
nobillygreen
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Python Library for installation of Graph tool

In order to install Graph-tool, I have first installed pythons 3.2 and C++ boost library boost_1_56_0. However when I run ./configure for graph tool. I got the following error: checking for boostlib >= 1.53.0... yes checking whether the…
user3356568
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Changing background color in graph-tool

I'm setting about to use a python package named graph-tool to visualize graphs. For some reason it sets grey background color each time saving a graph, which looks far from pleasant. Anyone knows how to change it to white? For example, this sample…
kurtosis
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Graph_Tool - Draw Graph with user defined vertex text

Im trying to set text in different vertexs and draw them, but I don't know how to make it. I searched graph_tool documentaction but I can't find out how to make it because examples there are so confused... My code is: from graph_tool.all import * g…
rafixwpt
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GCC consumes too much Memory!! graph-tool

While Compiling graph-tool the gcc-compiler consumes more than 7 Gb of memory and after consuming more and more nothing happens anymore and I am forced to stop the compilation. I tried to embed a compiler suffix: CFLAGS="$CFLAGS --param…
varantir
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