Igraph Layout Examples

4 Date Oct 3, 2007 Title Routines for simple graphs, network analysis. The igraph R package features an interactive graph layout editor for small graphs. Skip navigation Sign in. 8 Plotting two-mode networks 4. 6 Interactive plotting with tkplot 4. directed as_edgelist as_graphnel as_ids as. A matrix with two columns and as many lines as the total number of vertices in the graphs. iGraph offers many different graph layouts to experiment from. Network Topologies • Topology -Physical and logical network layout –Physical –actual layout of the computer cables and other network devices –Logical –the way in which the network appears to the devices that use it. References. layout Same as in qgraph repulsion The repulsion parameter as used in qgraph. palette = 0 uncolored (white) boxes (default for prp) box. Contribute to igraph/igraph development by creating an account on GitHub. Library for the analysis of networks. Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a. Other layouts. , and thus, it is not surprising that network visualization is a hot. The default layout and attributes are not very pretty. Most of the functions return a 'tibble' object (enhancement of 'dataframe') which can be used for further analysis. igraph_layout_random — Places the vertices uniform randomly on a plane. Draw(layout); } This design works pretty fine. For standard node-edge diagrams igraph defines a long range of different layout functions that are all available through the igraph layout where the specific layout is specified using the algorithm argument. Calculate Cohesive Blocks. Whether to make 2d or a 3d layout Passed to layout_on_grid. Find the function on each end of the interval. So, with a circular graph layout, how to get the labels aligned nicely? Here’s an approach that I think will work, and should generalize to however many vertices you have around the circle. To convert an igraph graph to pajek format simply use write. Can you move some of the vertices or bend. Since igraph and statnet do the plotting using base system graphics, we can’t put everything in the same device right away. Place vertices on a circle, in the order of their vertex ids. It accepts either a general numerical data matrix, a distance matrix, or a correlation matrix as input data, and outputs two nFCA graphs, a H-graph and an I-graph that reveal systematic, hierarchical clustering and inherent structure of the data. The package offers functions to produce 'network' and 'igraph' dependency graphs. For example:. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community structure search. To show this we take a look at some colonial Americans:. Understanding information flow and dominant contributions to an overall flow are critical aspects for analyzing efficiency or lack thereof in. NETWORK REPRESENTATION WITH IGRAPH , R Charts, Servers. svd: SVD layout, this was removed from igraph: layout_ Graph layouts: layout_as_bipartite: Simple two-row layout for bipartite graphs: layout_as_star. Additional information can be found on this guide to igraph which is in development, the examples here, and the official CRAN documentation of the package. Network visualization with R Katherine Ognyanova,www. igraph { software package for complex network research Tam as Nepusz1;2, G abor Cs ardi2;3 1Dept. 4 Date Oct 3, 2007 Title Routines for simple graphs, network analysis. The plot has been done entirely in R (2. igraph(g,vertex. Here are some examples. graphopt is a port of the graphopt layout algorithm by Michael Schmuhl. The igraph library provides versatile options for descriptive network analysis and visualization in R, Python, and C/C++. plot(X, layout=z) A walk on Python-igraph 20/46. Graph-based two-sample tests were introduced by Friedman and Rafsky 25 as a generalization of the Wald-Wolfowitz runs test. $\endgroup$ – Andy W Feb 26 '15 at 21:22 1 $\begingroup$ IMHO there is only one cluster in this graph. bg, layout=l) The available graphopt. by) Arguments g graph (igraph) to layout. Most functions have corresponding demo(), see documentation and shiny demo. It is defined as the drop in the Laplacian energy (i. Many graphs use a time series, meaning they measure events over time. 5-1 Date 2013-02-27 Title Network analysis and visualization Author See AUTHORS file. Another example is visualizing metabolic pathways - there you also have to minimize the edge overlaps and present the layout in a more symmetric manner with specific labels. Note that you need to threshold the p-value matrix at the desired cut-off and to convert it into a network using a script of your own. Example: Creating an empty network in Cytoscape from Python Without py2cytoscape (raw cyREST API call). by Yanchang Zhao, RDataMining. Everything flows and Flow is everything. However, the neato, twopi, and circo layouts are selectable by setting the graph attribute layout equal to either neato, twopi, or circo in a Graphviz graph. To do that we need layout algorithms in which we can specify the initial positions of the nodes and let the algorithm evolve smoothly from that initial position. In this blog, I would like to share another approach that uses R in Tableau to create a dynamic network graph. of Measurement and Information Systems Budapest University of Technology and Economics, Budapest, Hungary 2Dept. js force layout. It is tested on di erent Linux avors, Mac OS X, MS Windows and Sun OS. For example, if you tried it on a transcriptome of 20,000 protein-coding genes, you would have to generate a distance matrix of 400,000,000 data points. Network layouts are algorithms that return coordinates for each node in a network. As a minor side note: If you ever struggle with anything in igraph, consult the excellent tutorial from Katherine Ognyanova. Delta ICP015 & Igraph I have an ICP015 Rev3. Example sealed class SealedClass { public int x; public int y; } class SealedTest2 { static void Main() { var sc = new SealedClass(); sc. The following examples should allow you to get started and master the most common tasks concerning graph building. 4 igraph-package igraph-package The igraph package Introduction The main goals of the igraph library is an open source is to provide a set of data types and functions for 1) pain-free implementation of graph algorithms, 2) fast handling of large graphs, with millions of vertices and edges, 3) allow rapid prototyping via high level languages like R. The video and written tutorials on this page are primarily designed for users who are new to Shiny and want a guided introduction. by Yanchang Zhao, RDataMining. 4, vsize = 1. It's in GML format, so we'll need to specify that when we use read_graph(). See below for more on the object structure, or just check out the included example. igraph_layout_grid — Places the vertices on a regular grid on the plane. This video is unavailable. The plot has been done entirely in R (2. 5-1 Date 2013-02-27 Title Network analysis and visualization Author See AUTHORS file. The layout function in this package is a little more involved than the two-column matrix used by igraph. You can use a class to set the style on blocks of text. net NetSciX 2016 School of Code Workshop, Wroclaw, Poland Contents 1. Mathematica already has extensive graph theory and network analysis functionality, and IGraph/M does not aim to replace this. Topcoder is a crowdsourcing marketplace that connects businesses with hard-to-find expertise. If I used the output of just create_layout() below, I would get the same graph. Introduction to igraph (v. Vast amounts of network data are being generated and collected. In order to minimize typing all igraph algorithms can also be passed directly into the layout argument. An example of such situation is if the graph is bipartite. The igraph Package October 3, 2007 Version 0. To get started with IPython in the Jupyter Notebook, see our official example collection. Visual Awesomeness Unlocked – Sankey diagram. In addition to the layout choices provided by igraph, ggraph also implements its own layouts. In order to address these problems, we have made significant efforts in implementing all representative indexing methods on a common framework called iGraph. For example, the ability to and social networks were created using the R package igraph 60. a nodes data. seed(432104) n <- 1000 x <- rnorm(n, 0, 5) Most JAGS/BUGS examples save the probability model in a separate file and then read it in in the call to JAGS. Introduction To Igraph and Shiny out of the math domain primarily by social scientists For example Sampson (1968) did a social network analysis on monks in a. In the following example if the variable NumOfNodes is setted to a small value (10) the layout function generates a. Description. Details One convenient way to plot graphs is to plot with tkplot first, handtune the placement of the vertices, query the coordinates by the tk_coords function and use them with plot to plot the graph to any R device. It is easy to understand. igraph: Network Analysis and Visualization. params: Extra parameters in a list, to pass to the layout function. layout_igraph_backbone(g, keep = 0. However, if you supply a vector of edge ids, it will not work - it just returns the vertices for only the first edge, as can be seen from the below output:. Network Analysis Using R and igraph Young W. Figure 7: Example 5. Examples of SNA in R Additional Resources SNA Software Landscape Pros and Cons of R Comparison of SNA in R vs. CSS Grid Layout excels at dividing a page into major regions or defining the relationship in terms of size, position, and layer, between parts of a control built from HTML primitives. 0), has two steps, and it is more flexible. The first way is to call a layout function (they all have prefix layout_ on a graph, to get the vertex coordinates. Object settings. New to Plotly? Plotly's R library is free and open source! Get started by downloading the client and reading the primer. For details see the help page and Section 7. Tutorial Igraph with Python. 1 Title Network Analysis and Visualization Author See AUTHORS file. You'll use the igraph package to create networks from edgelists and adjacency matrices. Hierarchical Layout. Everything flows and Flow is everything. But what if my data is not hierarchical, you ask. ForceAtlas2 is a very fast layout algorithm for force directed graphs. 0), has two steps, and it is more flexible. igraph(g,vertex. Understanding information flow and dominant contributions to an overall flow are critical aspects for analyzing efficiency or lack thereof in. The default layout and attributes are not very pretty. Some are already available on the repository, for animating the graph or apply a force-directed layout to your graph. It is tested on di erent Linux avors, Mac OS X, MS Windows and Sun OS. The data analysis language R provides a rich and varied environment. Tutorial Igraph with Python. For example:. Type in the cell range of your data in the Input Range box under Input. frame function in the igraph packaage creates network objects. You can use a class to set the style on blocks of text. io Find an R package R language docs Run R in your browser R Notebooks. 5-1 Date 2013-02-27 Title Network analysis and visualization Author See AUTHORS file. Using layouts such as fruchterman. Draw(layout); } This design works pretty fine. rad: The degree to rotate the plot, in radian. Introduction to NetworkX - network analysis. layout_with_gem: The GEM layout algorithm in igraph: Network Analysis and Visualization rdrr. Examples of edge attributes are data associated with edges: most commonly edge weights, or visu-alization parameters. No direct support for bipartite (two-mode) graphs. Collector's Corner. pajek runs nicely in the wine. Examples of network structures, include: social media networks, friendship networks, collaboration networks and disease transmission. Visual Awesomeness Unlocked – Sankey diagram. A quick example on a synthetic network¶ We have recently developed a statistical framework to quantify biases of(in) rankings [1]. The adjacency matrix, sometimes also called the connection matrix, of a simple labeled graph is a matrix with rows and columns labeled by graph vertices, with a 1 or 0 in position according to whether and are adjacent or not. デフォルトではプロットの際にノードはランダムに配置される.ノードの配置はplot()のlayout引数にノードの座標を与えることで操作できるが,この座標をアルゴリズムによって決定し出力する関数がいくつか用意されている.これらの関数はlayout. Add routines to convert Sage graphs into igraph and viceversa. The first way is to call a layout function (they all have prefix layout_ on a graph, to get the vertex coordinates. The corresponding interface is: The corresponding interface is: public interface IVertexListGraph : IGraph // this interface defines the Graph conecpt { IVertex AddVertex(); void RemoveVertex(IVertex u); }. Thanks, this sounds insanely complicated. net POLNET 2015 Workshop, Portland OR Contents Introduction: NetworkVisualization2 Dataformat,size,andpreparation4. Depending upon the size of a given network different layouts may be more effective in communicating the structure of the network. The review of Igraph tutorial was not enough and the search in code communities started. Add routines to convert Sage graphs into igraph and viceversa. There are not two cohesive subgroups here as claimed by most analysts, but one (red:k=4 cohesive block,with k=3 and k=2 peripheries. bg) plot(net. The igraph software package for complex network research 3 Portability. If true the batch will be executed, otherwise only the undo units will be added. For better layouts, use one of these: plot. You can set up Plotly to work in online or offline mode. hu Department of Biophysics, KFKI Research Institute for Nuclear and Particle Physics of the Hungarian Academy of Sciences, Budapest, Hungary Currently at Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland. This is a very simplistic model and it does not, for example, take into account the importance of time dynamic effects in the virus spread. 2) clusters = graph. For example:. Author Gabor Csardi Maintainer Gabor Csardi Description Routines for simple graphs and network analysis. For most types of data storage, there is the concept of some elements of data (whether they be for example data nodes or data tables) having more precedence, or importance, over other elements. Egonet visualization in igraph. x}, y = {sc. For example, you can add or remove nodes or edges, determine the shortest path between two nodes, or locate a specific node or edge. •Technology: Internet routers, vehicular flows, power grids. For example, for a silly 4 node graph:. tilford: Deprecated layout functions: layout. Disadvantages of Bus Topology. For graphs with <100 nodes, the default layout in igraph 0. where 'my-selector' is where you want to place igraph, and myGraph is a plain ol' object. Use a igraph layout for compute coordinates & fast rendering. com This post presents an example of social network analysis with R using package igraph. 4 Plotting networks with igraph 4. kawai) plot. 01) with the help of the igraph package. The same AAA insertion described in cerebellum and cortex samples was also recorded with a lower frequency in spinal cord sample (21%), in the optic nerve (2. geom_bar() makes the height of the bar proportional to the number of cases in each group (or if the weight aesthetic is supplied, the sum of the weights). This function affect x and y coordinates to nodes data. reingold) > iGraph also provide various convenient ways to create patterned graphs some specific. x = 110; sc. Find the function on each end of the interval. This article is a follow on to my previous article on analyzing data with python. hu Department of Biophysics, KFKI Research Institute for Nuclear and Particle Physics of the Hungarian Academy of Sciences, Budapest, Hungary Currently at Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland. Network Analysis and Visualization with R and igraph Katherine Ognyanova,www. GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Description Calculates cohesive blocks for objects of class igraph. Figuerola: A walk on Python-igraph Plotting graphs making graphics from graphs is not the best of igraph library we can do graphics in two simple steps: · · choosing a layout (algorithm), it have several layouts availables applying such layout to our graph--z=X. Graph Concepts in igraph For example, the three neighbors of vertex 5 in our toy graph g are. graphopt version 0. Can be either an 1782 explicitly specified layout (using a list of coordinate 1783 pairs) or the name of a layout algorithm (which should 1784 refer to a method in the L{Graph} object, but without 1785 the C{layout_} prefix. GitHub Gist: instantly share code, notes, and snippets. Large-Scale Social Network Analysis with the igraph Toolbox and Signal/Collect András Heé of Zurich, Switzerland Student-ID: 08-982-142 andras. 4, vsize = 1. It is a great package but I found the documentation somewhat difficult to use, so hopefully this post can be a helpful introduction to network visualization with R. How to plot a SQL Server 2017 graph database using SQL Server R January 3, 2018 by Sifiso W. 4 Plotting networks with igraph 4. This is an example where the lack of subgrid became an issue. layout('fr') igraph. Everything flows and Flow is everything. hist2d (x, y) Customizing your histogram ¶ Customizing a 2D histogram is similar to the 1D case, you can control visual components such as the bin size or color normalization. It is possible to handle them via graph attributes. In this post, we’ll cover the community detection algorithms (~i. Hierarchical Layout. 8 Plotting two-mode networks 4. With the tidygraph package, you can easily manipulate the nodes and the edges data in the network graph object using dplyr verbs. It is a great package but I found the documentation somewhat difficult to use, so hopefully this post can be a helpful introduction to network visualization with R. Kaod aDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame,. Tutorial Igraph with Python. : coords <- layout. ForceAtlas2 is a very fast layout algorithm for force directed graphs. The following are top voted examples for showing how to use org. igraph Sample code This page showcases several screenshots and sample code for producing the images seen in the screenshots. This is already the case in the first igraph-object that we created, namely emailNW. The adjacency matrix, sometimes also called the connection matrix, of a simple labeled graph is a matrix with rows and columns labeled by graph vertices, with a 1 or 0 in position according to whether and are adjacent or not. Finally use a layout algorithm that uses weights like layout_with_fr (the new name of fruchterman. It basically allows to build any type of network with R. Co-occurrence can mean two words occurring together in the same document. For example:. Nemiroffc, and David L. It is only used as an argument for plotting. Examples of network structures, include: social media networks, friendship networks, collaboration networks and disease transmission. Many thanks. In my an application I have a function to plot stars with varying distances between the center of the star and the peripheral. An XML document typically contains nodes of information each with a parent node. Finally it merges the layouts via calling layout. Things start to get more interesting in the next example. Mathematica already has extensive graph theory and network analysis functionality, and IGraph/M does not aim to replace this. igraph_layout_star — Generate a star-like layout 1. The aim of this article is to describe 5+ methods for drawing a beautiful dendrogram using R software. Try plot_net with the default settings. In addition to the widgets featured below you may also want to check out the htmlwidgets gallery. 0), has two steps, and it is more flexible. #' plot_network(sel_triatomines = c(289)) - #' To plot the Triatoma pallidipenis interaction network #' #' @param sel_triatomines - Defines which triatomines to include in a list. NetworkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. New to Plotly? Plotly's R library is free and open source! Get started by downloading the client and reading the primer. For example, the VertexList concept defines the add_vertex and remove_vertex methods and refines the graph concepts. If you find the materials useful, please cite them in your work - this helps me make the case that open publishing of digital materials like this is a meaningful academic contribution: Ognyanova, K. Network Analysis and Visualization with R and igraph Katherine Ognyanova, www. Type in the cell range of your data in the Input Range box under Input. In this movie, I will show you how to download and ready for use the sna and igraph modules. Thanks, this sounds insanely complicated. 编者按:上个月菌群月坛,在军科院听取王军组陈亮博士分享网络分析的经验,不仅使我对网络的背景知识有了更全面的认识,更使我手上一个关于菌根的课题有极大的启示。. Learn Shiny. sg_get_layout helper to get graph's x and y positions. In igraph, this can be done for the Graphopt (layout_with_graphopt), Kamada-Kawai (layout_with_kk) and Fruchterman-reingold (layout_with_fr) algorithms using the coords or start argument:. First you call a layout specification function (the one without the layout_ prefix, and then layout_ (or add_layout_ ) to perform the layouting. Package ‘igraph’ April 22, 2019 Version 1. The aim of this article is to describe 5+ methods for drawing a beautiful dendrogram using R software. I don’t understand why someone would discontinue such a useful parameter, it’s not very user-friendly. With great htmlwidgets, it’s also possible to build custom shiny input from visNetwork. plot (g) There are several different options you can use to manipulate the graphical forms. The igraph package is the most important R package when it comes to build network diagrams with R. Additionally, ggraph provides a lot of new layout types and algorithms for your drawing pleasure. The resulting chart is a highchart object so you can keep modifying with the implmented API. Course Description. community_spinglass() # Specify initial layout: layout = None # Set up the video encoder: encoder = MEncoderVideoEncoder(bbox = (600, 600), fps = 30) encoder. Eventually they may end up in a blog post that wraps everything together. Delta ICP015 & Igraph I have an ICP015 Rev3. Note that if the matrix is unweighted, each connection can have only 2 values: 1 if there is a connection, 0 otherwise. Graph visualization is a way of representing structural information as diagrams of abstract graphs and 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. 4 igraphのネットワークデータセット(igraphdataパッケージ). 4 Date Oct 3, 2007 Title Routines for simple graphs, network analysis. Details One convenient way to plot graphs is to plot with tkplot first, handtune the placement of the vertices, query the coordinates by the tk_coords function and use them with plot to plot the graph to any R device. For example, for a silly 4 node graph:. BFS is the most commonly used approach. For details see the help page and Section 7. rad: The degree to rotate the plot, in radian. json for configuration files written in JSON format *. This tutorial covers basics of network analysis and visualization with the R package igraph (maintained by Gabor Csardi and Tamas Nepusz). Hierarchical Layout. You can change the layout by specifying different algorithms. Example of modularity measurement and colouring on a scale-free network. From now on, every example in the documentation will assume that igraph's objects and methods are imported into the main namespace (i. io Find an R package R language docs Run R in your browser R Notebooks. graphopt is a port of the graphopt layout algorithm by Michael Schmuhl. Please sign up to review new features, functionality and page designs. NETWORK REPRESENTATION WITH IGRAPH , R Charts, Servers. Usage cohesive. model package. R tutorials. graphopt is a port of the graphopt layout algorithm by Michael Schmuhl. 1 control panel with Igraph 2. The igraph library and the igraph R package do not introduce a new file format to store graphs. Visualize co-occurrence graph from document occurrence input using R package 'igraph' Wednesday January 30, 2013. by) Arguments g graph (igraph) to layout. Join GitHub today. by Yanchang Zhao, RDataMining. It can be started via either the graphical user interface or the R command line, as for example: # Start dynamic layout > relax(rdp, ps=TRUE) # Reset graph > resetd(rdp) The user can observe all steps of the layout optimization process and, at any particular time, the process can be driven interactively. js force layout. igraph network layouts The igraph package provides several built in layout algorithms for network visualization. Finally use a layout algorithm that uses weights like layout_with_fr (the new name of fruchterman. For example:. If you use Shiny on a regular basis, you may want to skip these tutorials and visit the articles section where we cover individual Shiny topics at a more advanced level. Introduction. write_svg(’first. Choose your layout using the layout argument. The layout specific settings used for. reingold) Acciaiuoli Albizzi Barbadori # plot igraph object g with xyz layout plot(g, layout. If network traffic is heavy or nodes are more the performance of the network decreases. Hierarchical Layout. This implies, for example, that the number of triangles in an undirected graph G is exactly the trace of A3 divided by 6. Easy to expand joining two cables together. Additionally, ggraph provides a lot of new layout types and algorithms for your drawing pleasure. The department of Policy Analysis and Management accommodates more than 30 faculty members with expertise in a variety of disciplines, including economics, sociology, demography, political science, public health, and public policy. 2 コミュニティーごとに色分け. In your example, you used qgraph( graph = “cor”) to create a correlation network. The example below uses Blondel and co-authors’ fast community detection algorithm implemented by igraph’s cluster_louvain() function to segment the thresholded precision matrix of stocks into groups. DFS for a connected graph produces a tree. Use a igraph layout for compute coordinates & fast rendering. Practical statistical network analysis (with R and igraph) G´abor Cs´ardi [email protected] Secondly, igraph layout functions can now be used directly in the layout argument (they were usable before in that their output was compatible with qgraph). 4C-seq Protocol and Primer Design. size=3,vertex. IGraph/M is a bit different from the official igraph interfaces (for C, Python and R). for cleaner-looking. I am wondering if there is any particular reason that you create a graph with qgraph instead of using functions in the igraph package, for example, “graph_from_adjacency_matrix()” function. I don’t understand why someone would discontinue such a useful parameter, it’s not very user-friendly. I have fixed the row heights just to match the Susy example. Learn how to make Sankey Diagram in Tableau through this amazing tutorial! Get the dataset and workbook: Pricing Design Work & Creativity - Duration: 36:30. maxiter: The maximum number of iterations to perform. A place to post R stories, questions, and news, For posting problems, Stack Overflow is a better platform, but feel free to cross post them here or on #rstats (Twitter). The following examples should allow you to get started and master the most common tasks concerning graph building. So, your data links will need to start from 0. Graph layout with vertices on a circle. To do that we need layout algorithms in which we can specify the initial positions of the nodes and let the algorithm evolve smoothly from that initial position. •Sociology: web pages, mobile phones, social networks. I have already run R, and what I'd like to do is see if I have either sna or igraph installed locally, and if not, then I can reach out onto the Internet to download them. 4 Highlighting aspects of the network 4. Define styles for edges, arrows, and nodes circle style for the main nodes, and font options so we don't need to adjust fonts within the nodes; For arrows, we use stealth' which is the name for a kind of arrow tip and shorten to not touch the node. net NetSciX 2016 School of Code Workshop, Wroclaw, Poland Contents. Place vertices on a circle, in the order of their vertex ids. A matrix with two columns and as many lines as the total number of vertices in the graphs. fig, ax = plt. The igraph Package October 3, 2007 Version 0. It addresses the many issues with construcing a d3 force-directed graph, allowing for easier customization and a more intuitive way. js force layout. python-igraph example. iASeq: integrating multiple sequencing datasets for detecting allele-specific events. Here are some examples. Other layouts. Matrix powers. Choose an output location under Output Options. Igraph can read and write Pajek and GraphML files, as well as simple edge lists. igraph and plotting connected components. Using Igraph to Mine Graph Analysis 1 [4] 3 -> 2 > plot(g, layout=layout. bg, layout=l) Graphopt is a nice force-directed layout implemented in igraph that uses layering to help with visualizations of large networks. Learn Shiny. The tbl_graph object. It also supports Barnes Hut approximation for maximum speedup. If you want to control the width of edges according to a variable, you should include the column "width" in the edge list data.