Representing Graphs and Hypergraphs by Touching Polygons in 3D William Evans 1 Paweł Rzążewski 2,3 Noushin Saeedi 1 Chan-Su Shin 4 Alexander Wolff 5
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Networkx Tutorial
5.03.2020 tutorial NetworkX tutorial Source: https://github.com/networkx/notebooks (https://github.com/networkx/notebooks) Minor corrections: JS, 27.02.2019 Creating a graph Create an empty graph with no nodes and no edges. In [1]: import networkx as nx In [2]: G = nx.Graph() By definition, a Graph is a collection of nodes (vertices) along with identified pairs of nodes (called edges, links, etc). In NetworkX, nodes can be any hashable object e.g. a text string, an image, an XML object, another Graph, a customized node object, etc. (Note: Python's None object should not be used as a node as it determines whether optional function arguments have been assigned in many functions.) Nodes The graph G can be grown in several ways. NetworkX includes many graph generator functions and facilities to read and write graphs in many formats. To get started though we'll look at simple manipulations. You can add one node at a time, In [3]: G.add_node(1) add a list of nodes, In [4]: G.add_nodes_from([2, 3]) or add any nbunch of nodes. An nbunch is any iterable container of nodes that is not itself a node in the graph. (e.g. a list, set, graph, file, etc..) In [5]: H = nx.path_graph(10) file:///home/szwabin/Dropbox/Praca/Zajecia/Diffusion/Lectures/1_intro/networkx_tutorial/tutorial.html 1/18 5.03.2020 tutorial In [6]: G.add_nodes_from(H) Note that G now contains the nodes of H as nodes of G. In contrast, you could use the graph H as a node in G. -
Networkx: Network Analysis with Python
NetworkX: Network Analysis with Python Salvatore Scellato Full tutorial presented at the XXX SunBelt Conference “NetworkX introduction: Hacking social networks using the Python programming language” by Aric Hagberg & Drew Conway Outline 1. Introduction to NetworkX 2. Getting started with Python and NetworkX 3. Basic network analysis 4. Writing your own code 5. You are ready for your project! 1. Introduction to NetworkX. Introduction to NetworkX - network analysis Vast amounts of network data are being generated and collected • Sociology: web pages, mobile phones, social networks • Technology: Internet routers, vehicular flows, power grids How can we analyze this networks? Introduction to NetworkX - Python awesomeness Introduction to NetworkX “Python package for the creation, manipulation and study of the structure, dynamics and functions of complex networks.” • Data structures for representing many types of networks, or graphs • Nodes can be any (hashable) Python object, edges can contain arbitrary data • Flexibility ideal for representing networks found in many different fields • Easy to install on multiple platforms • Online up-to-date documentation • First public release in April 2005 Introduction to NetworkX - design requirements • Tool to study the structure and dynamics of social, biological, and infrastructure networks • Ease-of-use and rapid development in a collaborative, multidisciplinary environment • Easy to learn, easy to teach • Open-source tool base that can easily grow in a multidisciplinary environment with non-expert users -
The Circle Packing Theorem
Alma Mater Studiorum · Università di Bologna SCUOLA DI SCIENZE Corso di Laurea in Matematica THE CIRCLE PACKING THEOREM Tesi di Laurea in Analisi Relatore: Pesentata da: Chiar.mo Prof. Georgian Sarghi Nicola Arcozzi Sessione Unica Anno Accademico 2018/2019 Introduction The study of tangent circles has a rich history that dates back to antiquity. Already in the third century BC, Apollonius of Perga, in his exstensive study of conics, introduced problems concerning tangency. A famous result attributed to Apollonius is the following. Theorem 0.1 (Apollonius - 250 BC). Given three mutually tangent circles C1, C2, 1 C3 with disjoint interiors , there are precisely two circles tangent to all the three initial circles (see Figure1). A simple proof of this fact can be found here [Sar11] and employs the use of Möbius transformations. The topic of circle packings as presented here, is sur- prisingly recent and originates from William Thurston's famous lecture notes on 3-manifolds [Thu78] in which he proves the theorem now known as the Koebe-Andreev- Thurston Theorem or Circle Packing Theorem. He proves it as a consequence of previous work of E. M. Figure 1 Andreev and establishes uniqueness from Mostov's rigid- ity theorem, an imporant result in Hyperbolic Geometry. A few years later Reiner Kuhnau pointed out a 1936 proof by german mathematician Paul Koebe. 1We dene the interior of a circle to be one of the connected components of its complement (see the colored regions in Figure1 as an example). i ii A circle packing is a nite set of circles in the plane, or equivalently in the Riemann sphere, with disjoint interiors and whose union is connected. -
Planar Graph Theory We Say That a Graph Is Planar If It Can Be Drawn in the Plane Without Edges Crossing
Planar Graph Theory We say that a graph is planar if it can be drawn in the plane without edges crossing. We use the term plane graph to refer to a planar depiction of a planar graph. e.g. K4 is a planar graph Q1: The following is also planar. Find a plane graph version of the graph. A B F E D C A Method that sometimes works for drawing the plane graph for a planar graph: 1. Find the largest cycle in the graph. 2. The remaining edges must be drawn inside/outside the cycle so that they do not cross each other. Q2: Using the method above, find a plane graph version of the graph below. A B C D E F G H non e.g. K3,3: K5 Here are three (plane graph) depictions of the same planar graph: J N M J K J N I M K K I N M I O O L O L L A face of a plane graph is a region enclosed by the edges of the graph. There is also an unbounded face, which is the outside of the graph. Q3: For each of the plane graphs we have drawn, find: V = # of vertices of the graph E = # of edges of the graph F = # of faces of the graph Q4: Do you have a conjecture for an equation relating V, E and F for any plane graph G? Q5: Can you name the 5 Platonic Solids (i.e. regular polyhedra)? (This is a geometry question.) Q6: Find the # of vertices, # of edges and # of faces for each Platonic Solid. -
Graphprism: Compact Visualization of Network Structure
GraphPrism: Compact Visualization of Network Structure Sanjay Kairam, Diana MacLean, Manolis Savva, Jeffrey Heer Stanford University Computer Science Department {skairam, malcdi, msavva, jheer}@cs.stanford.edu GraphPrism Connectivity ABSTRACT nodeRadius 7.9 strokeWidth 1.12 charge -242 Visual methods for supporting the characterization, com- gravity 0.65 linkDistance 20 parison, and classification of large networks remain an open Transitivity updateGraph Close Controls challenge. Ideally, such techniques should surface useful 0 node(s) selected. structural features { such as effective diameter, small-world properties, and structural holes { not always apparent from Density either summary statistics or typical network visualizations. In this paper, we present GraphPrism, a technique for visu- Conductance ally summarizing arbitrarily large graphs through combina- tions of `facets', each corresponding to a single node- or edge- specific metric (e.g., transitivity). We describe a generalized Jaccard approach for constructing facets by calculating distributions of graph metrics over increasingly large local neighborhoods and representing these as a stacked multi-scale histogram. MeetMin Evaluation with paper prototypes shows that, with minimal training, static GraphPrism diagrams can aid network anal- ysis experts in performing basic analysis tasks with network Created by Sanjay Kairam. Visualization using D3. data. Finally, we contribute the design of an interactive sys- Figure 1: GraphPrism and node-link diagrams for tem using linked selection between GraphPrism overviews the largest component of a co-authorship graph. and node-link detail views. Using a case study of data from a co-authorship network, we illustrate how GraphPrism fa- compactly summarizing networks of arbitrary size. Graph- cilitates interactive exploration of network data. -
Graph Simplification and Interaction
Graph Clarity, Simplification, & Interaction http://i.imgur.com/cW19IBR.jpg https://www.reddit.com/r/CableManagement/ Today • Today’s Reading: Lombardi Graphs – Bezier Curves • Today’s Reading: Clustering/Hierarchical edge Bundling – Definition of Betweenness Centrality • Emergency Management Graph Visualization – Sean Kim’s masters project • Reading for Tuesday & Homework 3 • Graph Interaction Brainstorming Exercise "Lombardi drawings of graphs", Duncan, Eppstein, Goodrich, Kobourov, Nollenberg, Graph Drawing 2010 • Circular arcs • Perfect angular resolution (edges for equal angles at vertices) • Arcs only intersect 2 vertices (at endpoints) • (not required to be crossing free) • Vertices may be constrained to lie on circle or concentric circles • People are more patient with aesthetically pleasing graphs (will spend longer studying to learn/draw conclusions) • What about relaxing the circular arc requirement and allowing Bezier arcs? • How does it scale to larger data? • Long curved arcs can be much harder to follow • Circular layout of nodes is often very good! • Would like more pseudocode Cubic Bézier Curve • 4 control points • Curve passes through first & last control point • Curve is tangent at P0 to (P1-P0) and at P3 to (P3-P2) http://www.e-cartouche.ch/content_reg/carto http://www.webreference.com/dla uche/graphics/en/html/Curves_learningObject b/9902/bezier.html 2.html “Force-directed Lombardi-style graph drawing”, Chernobelskiy et al., Graph Drawing 2011. • Relaxation of the Lombardi Graph requirements • “straight-line segments -
Constraint Graph Drawing
Constrained Graph Drawing Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften vorgelegt von Barbara Pampel, geb. Schlieper an der Universit¨at Konstanz Mathematisch-Naturwissenschaftliche Sektion Fachbereich Informatik und Informationswissenschaft Tag der mundlichen¨ Prufung:¨ 14. Juli 2011 1. Referent: Prof. Dr. Ulrik Brandes 2. Referent: Prof. Dr. Michael Kaufmann II Teile dieser Arbeit basieren auf Ver¨offentlichungen, die aus der Zusammenar- beit mit anderen Wissenschaftlerinnen und Wissenschaftlern entstanden sind. Zu allen diesen Inhalten wurden wesentliche Beitr¨age geleistet. Kapitel 3 (Bachmaier, Brandes, and Schlieper, 2005; Brandes and Schlieper, 2009) Kapitel 4 (Brandes and Pampel, 2009) Kapitel 6 (Brandes, Cornelsen, Pampel, and Sallaberry, 2010b) Zusammenfassung Netzwerke werden in den unterschiedlichsten Forschungsgebieten zur Repr¨asenta- tion relationaler Daten genutzt. Durch geeignete mathematische Methoden kann man diese Netzwerke als Graphen darstellen. Ein Graph ist ein Gebilde aus Kno- ten und Kanten, welche die Knoten verbinden. Hierbei k¨onnen sowohl die Kan- ten als auch die Knoten weitere Informationen beinhalten. Diese Informationen k¨onnen den einzelnen Elementen zugeordnet sein, sich aber auch aus Anordnung und Verteilung der Elemente ergeben. Mit Algorithmen (strukturierten Reihen von Arbeitsanweisungen) aus dem Gebiet des Graphenzeichnens kann man die unterschiedlichsten Informationen aus verschiedenen Forschungsbereichen visualisieren. Graphische Darstellungen k¨onnen das -
Representing Graphs by Polygons with Edge Contacts in 3D
Representing Graphs by Polygons with Side Contacts in 3D∗ Elena Arseneva1, Linda Kleist2, Boris Klemz3, Maarten Löffler4, André Schulz5, Birgit Vogtenhuber6, and Alexander Wolff7 1 Saint Petersburg State University, Russia [email protected] 2 Technische Universität Braunschweig, Germany [email protected] 3 Freie Universität Berlin, Germany [email protected] 4 Utrecht University, the Netherlands [email protected] 5 FernUniversität in Hagen, Germany [email protected] 6 Technische Universität Graz, Austria [email protected] 7 Universität Würzburg, Germany orcid.org/0000-0001-5872-718X Abstract A graph has a side-contact representation with polygons if its vertices can be represented by interior-disjoint polygons such that two polygons share a common side if and only if the cor- responding vertices are adjacent. In this work we study representations in 3D. We show that every graph has a side-contact representation with polygons in 3D, while this is not the case if we additionally require that the polygons are convex: we show that every supergraph of K5 and every nonplanar 3-tree does not admit a representation with convex polygons. On the other hand, K4,4 admits such a representation, and so does every graph obtained from a complete graph by subdividing each edge once. Finally, we construct an unbounded family of graphs with average vertex degree 12 − o(1) that admit side-contact representations with convex polygons in 3D. Hence, such graphs can be considerably denser than planar graphs. 1 Introduction A graph has a contact representation if its vertices can be represented by interior-disjoint geometric objects1 such that two objects touch exactly if the corresponding vertices are adjacent. -
Characterizations of Restricted Pairs of Planar Graphs Allowing Simultaneous Embedding with Fixed Edges
Characterizations of Restricted Pairs of Planar Graphs Allowing Simultaneous Embedding with Fixed Edges J. Joseph Fowler1, Michael J¨unger2, Stephen Kobourov1, and Michael Schulz2 1 University of Arizona, USA {jfowler,kobourov}@cs.arizona.edu ⋆ 2 University of Cologne, Germany {mjuenger,schulz}@informatik.uni-koeln.de ⋆⋆ Abstract. A set of planar graphs share a simultaneous embedding if they can be drawn on the same vertex set V in the Euclidean plane without crossings between edges of the same graph. Fixed edges are common edges between graphs that share the same simple curve in the simultaneous drawing. Determining in polynomial time which pairs of graphs share a simultaneous embedding with fixed edges (SEFE) has been open. We give a necessary and sufficient condition for when a pair of graphs whose union is homeomorphic to K5 or K3,3 can have an SEFE. This allows us to determine which (outer)planar graphs always an SEFE with any other (outer)planar graphs. In both cases, we provide efficient al- gorithms to compute the simultaneous drawings. Finally, we provide an linear-time decision algorithm for deciding whether a pair of biconnected outerplanar graphs has an SEFE. 1 Introduction In many practical applications including the visualization of large graphs and very-large-scale integration (VLSI) of circuits on the same chip, edge crossings are undesirable. A single vertex set can be used with multiple edge sets that each correspond to different edge colors or circuit layers. While the pairwise union of all edge sets may be nonplanar, a planar drawing of each layer may be possible, as crossings between edges of distinct edge sets are permitted. -
Chapter 18 Spectral Graph Drawing
Chapter 18 Spectral Graph Drawing 18.1 Graph Drawing and Energy Minimization Let G =(V,E)besomeundirectedgraph.Itisoftende- sirable to draw a graph, usually in the plane but possibly in 3D, and it turns out that the graph Laplacian can be used to design surprisingly good methods. n Say V = m.Theideaistoassignapoint⇢(vi)inR to the vertex| | v V ,foreveryv V ,andtodrawaline i 2 i 2 segment between the points ⇢(vi)and⇢(vj). Thus, a graph drawing is a function ⇢: V Rn. ! 821 822 CHAPTER 18. SPECTRAL GRAPH DRAWING We define the matrix of a graph drawing ⇢ (in Rn) as a m n matrix R whose ith row consists of the row vector ⇥ n ⇢(vi)correspondingtothepointrepresentingvi in R . Typically, we want n<m;infactn should be much smaller than m. Arepresentationisbalanced i↵the sum of the entries of every column is zero, that is, 1>R =0. If a representation is not balanced, it can be made bal- anced by a suitable translation. We may also assume that the columns of R are linearly independent, since any basis of the column space also determines the drawing. Thus, from now on, we may assume that n m. 18.1. GRAPH DRAWING AND ENERGY MINIMIZATION 823 Remark: Agraphdrawing⇢: V Rn is not required to be injective, which may result in! degenerate drawings where distinct vertices are drawn as the same point. For this reason, we prefer not to use the terminology graph embedding,whichisoftenusedintheliterature. This is because in di↵erential geometry, an embedding always refers to an injective map. The term graph immersion would be more appropriate. -
Separator Theorems and Turán-Type Results for Planar Intersection Graphs
SEPARATOR THEOREMS AND TURAN-TYPE¶ RESULTS FOR PLANAR INTERSECTION GRAPHS JACOB FOX AND JANOS PACH Abstract. We establish several geometric extensions of the Lipton-Tarjan separator theorem for planar graphs. For instance, we show that any collection C of Jordan curves in the plane with a total of m p 2 crossings has a partition into three parts C = S [ C1 [ C2 such that jSj = O( m); maxfjC1j; jC2jg · 3 jCj; and no element of C1 has a point in common with any element of C2. These results are used to obtain various properties of intersection patterns of geometric objects in the plane. In particular, we prove that if a graph G can be obtained as the intersection graph of n convex sets in the plane and it contains no complete bipartite graph Kt;t as a subgraph, then the number of edges of G cannot exceed ctn, for a suitable constant ct. 1. Introduction Given a collection C = fγ1; : : : ; γng of compact simply connected sets in the plane, their intersection graph G = G(C) is a graph on the vertex set C, where γi and γj (i 6= j) are connected by an edge if and only if γi \ γj 6= ;. For any graph H, a graph G is called H-free if it does not have a subgraph isomorphic to H. Pach and Sharir [13] started investigating the maximum number of edges an H-free intersection graph G(C) on n vertices can have. If H is not bipartite, then the assumption that G is an intersection graph of compact convex sets in the plane does not signi¯cantly e®ect the answer. -
Colouring Contact Graphs of Squares and Rectilinear Polygons
Colouring contact graphs of squares and rectilinear polygons Citation for published version (APA): de Berg, M., Markovic, A., & Woeginger, G. (2016). Colouring contact graphs of squares and rectilinear polygons. In 32nd European Workshop on Computational Geometry (EuroCG 2016), 30 March - 1 April, Lugano, Switzerland (pp. 71-74) Document status and date: Published: 01/01/2016 Document Version: Publisher’s PDF, also known as Version of Record (includes final page, issue and volume numbers) Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal.