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  • Digital Humanities Workshop University of Rijeka 17-18 March, 2016

    Introduction to Data Visualization:

    Networks and Gephi

    Rocio Chongtay

    rocio@sdu.dk

  • Brief BioViz

    Born in Mexico

    BSc in Biology

    MSc

    Comp. Sci.

    Worked at Mexican

    University

    Moved to Edinburgh,

    UK

    MSc Information Tchnology

    PhD in Artificial

    Intellignece.

    Worked at Endinburgh

    University

    Moved to Copenhagen,

    Denmark

    Worked for Sotware Industry

    Current work at

    University Southern

    Denmark

    Born in

    Mexico

    BSc in

    Biology

    MSc

    Comp.

    Sci.

    MSc

    Information

    Tchnology

    Moved to

    Edinburgh,

    UK

    PhD in

    Artificial

    Intellignece

    Moved to

    Copenhagen,

    Denmark

    Worked for

    Sotware

    Industry

    Current Work

    U. Southern

    Denmark

    Worked at

    Mexican

    University

    Worked at

    Edinburgh

    University

  • Brief Bio

    Source: http://www.oecdbetterlifeindex.org/countries/denmark/

    Associate Professor at the Institute for Design and Communication

    At The University of Southern Denmark campus Kolding

    http://www.oecdbetterlifeindex.org/countries/denmark/http://www.oecdbetterlifeindex.org/countries/denmark/

  • Agenda

    Helicopter overview to network

    visualization

    Introduction to Gephi

    Hands on Gephi: a step by step tutorial

  • Helicopter overview of

    Network Visualization

  • Network Visualization

    A network is made of two components :

    1) a list of actors composing the network, and

    2) a list of the relations (the interactions between actors).

    As part of a mathematical object, actors will then be called vertices (nodes, in Gephi), and relations will be denoted as tiles (edges, in Gephi).

    Network analysis and visualization is considered a useful way to see

    data from a different angle.*

    Source: Grandjean, M. (2015) GEPHI Introduction to network analysis and

    visualization , http://www.martingrandjean.ch/gephi-introduction

    http://www.martingrandjean.ch/gephi-introductionhttp://www.martingrandjean.ch/gephi-introductionhttp://www.martingrandjean.ch/gephi-introduction

  • Network Visualization

    But lets back down a little

    and review the following

    networks features:

    Types

    Goals

    Controls

    sthetics

    Source: https://rpubs.com/kateto/netviz

    https://rpubs.com/kateto/netvizhttps://rpubs.com/kateto/netvizhttps://rpubs.com/kateto/netviz

  • Networks visualization

    Source: https://rpubs.com/kateto/netviz

    https://rpubs.com/kateto/netviz

  • What do you want to analyze?

    Source: https://rpubs.com/kateto/netviz

    https://rpubs.com/kateto/netvizhttps://rpubs.com/kateto/netviz

  • What visualization type fits best?

    Source: https://rpubs.com/kateto/netviz

  • Which controls you can use?

    Source: https://rpubs.com/kateto/netviz

  • Optimize looks for better vizualization

    Source: https://rpubs.com/kateto/netviz

  • Introduction to Gephi

  • Introduction to Gephi Gephi is a tool built with the idea of using visualization of graphs and

    networks for interactive exploration of data and data structures.

  • File formats supported by Gephi

    The recommended format if only working with Gephi is GEXF

  • Gephi user interface

  • Gephi user interface

  • Gephi user interface

    Edit

    graph

    tools

    Edit edge visibility, thinkness and

    labels text tools Expand

    settings

  • Edit graph tools

    Edit edge visibility, thinkness and

    labels text tools Expand

    settings

    The painter click and hold mouse

    button to color selected nodes.

    There is a pencil to create new nodes

    and one to create new edges (size

    and color)

    The airplane is to show the shortest

    path between 2 nodes (different for

    directed or non-directed graphs)

    The heatmap shows the distance

    from a single node point of view,

    highlights the closest and farthest

    reachable nodes

    The Edit graph tools allows to

    modify data directly from the

    visualizaton (overview) window.

    The arrow is used to select indivisual elements

    The rectangle is used to select one or multiple

    areas of the network

    Drag.is used to drag elements around

    Sizer resize nodes by pressing left mouse button

    and drag up or down

    Brush colors nodes and neighbours by clicking

    on them.

  • Gephi user interface

    Algorithm selection

    and parameters

    Layout algorithms Graphs are usually layout with Force-based algorithms. Their

    principle is easy, linked nodes attract each other and non-linked nodes are pushed apart.

  • Gephi user interface

    For example: Avg. Path Length: computes the path length for all possible pairs of

    nodes and give information about how nodes are close from each other: -

    Betweeness Centrality - Closeness Centrality - Eccentricity

    Metrics,

  • Gephi Algorithms

    Source: http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/

    Emphasis

    divisions

    Emphasis

    ranking

    Emphasis

    Geographic

    repartition

    Emphasis

    complementarities

    http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/http://www.slideshare.net/gephi/gephi-tutorial-layouts?ref=https://gephi.org/users/tutorial-layouts/

  • Input data for Gephi

    Data for use in Gephi can be input from:

    Directly within the program (Overview or Data

    Laboratory),

    imported from text files in a number of formats,

    Imported from relational databases, graph databases

    such as Neo4J,

    Data stores with import plugins.

  • Hands on Data Visualization

    The best way to understand Gephis interface and

    exploration potentials is with a simple example:

    Input data:

    Import data from CSV file

  • Gephis use case:

    Visualizing Historical Networks

    Source: http://www.fas.harvard.edu/~histecon/visualizing/index.html

    http://www.fas.harvard.edu/~histecon/visualizing/index.htmlhttp://www.fas.harvard.edu/~histecon/visualizing/index.html

  • Gephis use case:

    Visualizing Historical Networks

    Source: http://www.fas.harvard.edu/~histecon/visualizing/index.html

    http://www.fas.harvard.edu/~histecon/visualizing/index.htmlhttp://www.fas.harvard.edu/~histecon/visualizing/index.html

  • Gephis use case:

    Visualizing Historical Networks

    Source: http://www.fas.harvard.edu/~histecon/visualizing/index.html

    Downloading files:

    -nodes.csv

    -edges.csv

    http://www.fas.harvard.edu/~histecon/visualizing/index.htmlhttp://www.fas.harvard.edu/~histecon/visualizing/index.html

  • Gephis use case:

    Visualizing Historical Networks

    Source: http://www.fas.harvard.edu/~histecon/visualizing/index.html

    There is slight mistake in the

    -edges.csv file, you need to open it in Excel and change the name of the

    first two colums to Source and Target

    http://www.fas.harvard.edu/~histecon/visualizing/index.htmlhttp://www.fas.harvard.edu/~histecon/visualizing/index.html

  • Input data: import csv files

    2) Open Gephi and select a new project

    3) Click on the tab Data Laboratory

    Here you can see that Nodes tab is selected,

    4) so we click in Import Spreadsheet

  • Input data: import csv files

    5) On the Import spreadsheet window select the ...

    Button to select the location where you saved the

    nodes.csv file

  • Input data: import csv files 6) If your data doesnt look like a table with columns, then you

    need to choose the rigth separator, for example commas,

    semicolon, etc. Depending how the dada is saved in your file and

    what option was used last in Gephi:

    comma separated, change to Comma here Then Press Next

    If it already looks like this just press Next

  • Input data: import csv files

    7) Leave the import settings as they are, click Finish button

  • Input data: import csv files 8) Leave the import settings as they are, click Finish button,

    then you will see the data in a table like this

  • Input data: import csv files Press the tab Edges and repeat steps from 4-8

    You just need to

    remember to both

    Select the right file and

    change the type of table

  • Gephis use case:

    Visualizing Historical Networks

    Source: http://www.fas.harvard.edu/~histecon/visualizing/