248 search results for "igraph"

Gene homology Part 2 – creating directed networks with igraph

December 13, 2016
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Gene homology Part 2 – creating directed networks with igraph

In my last post I created a gene homology network for human genes. In this post I want to extend the network to include edges for other species. First, I am loading biomaRt and extract a list of all available datasets. library(biomaRt) ensembl = useM...

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Sunbelt and EUSN workshops on using R and ‘igraph’ for SNA

March 4, 2016
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I would like to (re)announce the workshop I will be giving on using R and ‘igraph’ for Social Network Analysis on the upcoming Sunbelt 2016 conference in Newport Beach. My goal is to provide gentle and practical tour through the SNA functionality of R package “igraph”. The exact date of the Sunbelt workshop is Tuesday

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Network analysis with igraph

June 23, 2015
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Network analysis with igraph

Suddenly, I had to learn network analysis. Two weeks ago I started with a book by Christakis and Fowler, then a book by Kolaczyk and Csárdi, now here I am in a “how to” analyse network data using R moment. This is much like learning-by-doing knowledge, so may be useful for newcomers, although at this … Read More...

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A look at the igraph package

November 13, 2014
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A look at the igraph package

by Joseph Rickert The igraph package has become a fundamental tool for the study of graphs and their properties, the manipulation and visualization of graphs and the statistical analysis of networks. To get an idea of just how firmly igraph has become embedded into the R package ecosystem consider that currently igraph lists 72 reverse depends, 59 reverse imports...

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Going viral with R’s igraph package

March 23, 2014
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Going viral with R’s igraph package

R's igraph package provides a simple and flexible set of utilities for working with graphs.  In this post, we'll use this package to animate the simulated spread of a disease through a network. Graphs A graph is just a collection of nodes joined by edges: require(igraph)# Specify an undirected graph by hand, using...

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Temporal network model – Barabási-Albert model with the library igraph

February 17, 2013
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I found a golden website. The blog of Esteban Moro. He uses R to work on networks. In particular he has done a really nice code to make some great videos of networks. This post is purely a copy of his code. I just changed a few arguments to change colors and to do my own network.To...

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igraph degree distribution: count elements

February 13, 2013
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Unfortunately, the degree.distribution() function of the igraph library returns the intensities of the distribution:> g > plot(g) > summary(g)IGRAPH U--- 10 10 -- Ring graphattr: name (g/c), mutual (g/x), circular (g/x) So instead of having the number of elements, the density/intensities value is returned:> degree.distribution(g) 0 0 1 You can easily verify this in the source code...

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Making prettier network graphs with sna and igraph

December 18, 2012
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Making prettier network graphs with sna and igraph

We’ve had some requests for ideas about how to make prettier network graphs, so here is one example, using the sna package for plotting, and the igraph package to calculate PageRank. The help file for gplot is pretty self-explanatory, but Melissa Clarkson has produced the most thorough and impressive guide for any R...

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R/iGraph Holiday network animation and How-to tips

December 17, 2012
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R/iGraph Holiday network animation and How-to tips

The animation embedded in this post was done using R and the iGraph package and was, frankly, a great deal more work than I thought it would be when I started. What kept me going was a desire to express a wish for the New Year while also experimenting with some functionality that might be

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Community detection algorithm with igraph and R – (2)

December 13, 2012
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In the last post I presented a slightly modified LPA algorithm from the igraph wiki. This algorithm needed around 40s for 10,000,000 edges and 1000 unique vertices. I promised, that one could do much better. Here you go!Iterators in igraphTo understand...

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