Pro Data Visualization using R and JavaScript Tom Barker Pro Data Visualization using R and JavaScript Copyright © 2013 by Tom Barker This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher's location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. ISBN-13 (pbk): 978-1-4302-5806-3 ISBN-13 (electronic): 978-1-4302-5807-0 Trademarked names, logos, and images may appear in this book. Rather than use a trademark symbol with every occurrence of a trademarked name, logo, or image we use the names, logos, and images only in an editorial fashion and to the benefit of the trademark owner, with no intention of infringement of the trademark. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. President and Publisher: Paul Manning Lead Editor: Ben Renow-Clarke Technical Reviewer: Matthew Canning Editorial Board: Steve Anglin, Mark Beckner, Ewan Buckingham, Gary Cornell, Louise Corrigan, Morgan Ertel, Jonathan Gennick, Jonathan Hassell, Robert Hutchinson, Michelle Lowman, James Markham, Matthew Moodie, Jeff Olson, Jeffrey Pepper, Douglas Pundick, Ben Renow-Clarke, Dominic Shakeshaft, Gwenan Spearing, Matt Wade, Tom Welsh Coordinating Editor: Christine Ricketts Copy Editor: Nancy Sixsmith Compositor: SPi Global Indexer: SPi Global Artist: SPi Global Cover Designer: Anna Ishchenko Distributed to the book trade worldwide by Springer Science+Business Media New York, 233 Spring Street, 6th Floor, New York, NY 10013. Phone 1-800-SPRINGER, fax (201) 348-4505, e-mail [email protected], or visit www.springeronline.com. Apress Media, LLC is a California LLC and the sole member (owner) is Springer Science + Business Media Finance Inc (SSBM Finance Inc). SSBM Finance Inc is a Delaware corporation. For information on translations, please e-mail [email protected], or visit www.apress.com. Apress and friends of ED books may be purchased in bulk for academic, corporate, or promotional use. eBook versions and licenses are also available for most titles. For more information, reference our Special Bulk Sales–eBook Licensing web page at www.apress.com/bulk-sales. Any source code or other supplementary materials referenced by the author in this text is available to readers at www.apress.com. For detailed information about how to locate your book’s source code, go to www.apress.com/source-code/. For my grandmother, Ann Biango, who passed away during the creation of this book. I was very lucky to have her in my life for as long as I did. Contents at a Glance About the Author About the Technical Reviewer Acknowledgments Chapter 1: Background Chapter 2: R Language Primer Chapter 3: A Deeper Dive into R Chapter 4: Data Visualization with D3 Chapter 5: Visualizing Spatial Data from Access Logs Chapter 6: Visualizing Data Over Time Chapter 7: Bar Charts Chapter 8: Correlation Analysis with Scatter Plots Chapter 9: Visualizing the Balance of Delivery and Quality with Parallel Coordinates Index Contents About the Author About the Technical Reviewer Acknowledgments Chapter 1: Background What Is Data Visualization? Time Series Charts Bar Charts Histograms Data Maps Scatter Plots History Modern Landscape Why Data Visualization? Tools Languages, Environments, and Libraries Analysis Tools Process Overview Identify a Problem Gather Data Analyze Data Visualize Data Ethics of Data Visualization Cite Sources Be Aware of Visual Cues Summary Chapter 2: R Language Primer Getting to Know the R Console The Command Line Command History Accessing Documentation Packages Importing Data Using Headers Specifying a String Delimiter Specifying Row Identifiers Using Custom Column Names Data Structures and Data Types Data Frames Matrices Adding Lists Looping Through Lists Applying Functions to Lists Functions Summary Chapter 3: A Deeper Dive into R Object-Oriented Programming in R S3 Classes S4 Classes Statistical Analysis with Descriptive Metrics in R Median and Mean Quartiles Standard Deviation RStudio IDE R Markdown RPubs Summary Chapter 4: Data Visualization with D3 Preliminary Concepts HTML CSS SVG JavaScript History of D3 Using D3 Setting Up a Project Using D3 Binding Data Creating a Bar Chart Loading External Data Summary Chapter 5: Visualizing Spatial Data from Access Logs What Are Data Maps? Access Logs Parsing the Access Log Read in the Access Log Parse the Log File Geolocation by IP Output the Fields Adding Control Logic Creating a Data Map in R Distributing the Visualization Summary Chapter 6: Visualizing Data Over Time Gathering Data Data Analysis with R Calculating the Bug Count Examining the Severity of the Bugs Adding Interactivity with D3 Reading in the Data Drawing on the Page Adding Interactivity Summary Chapter 7: Bar Charts Standard Bar Chart Stacked Bar Chart Grouped Bar Chart Visualizing and Analyzing Production Incidents Plotting Data on a Bar Chart with R Ordering Results Creating a Stacked Bar Chart Bar Charts in D3 Creating a Vertical Bar Chart Creating a Stacked Bar Chart Creating an Overlaid Visualization Summary Chapter 8: Correlation Analysis with Scatter Plots Finding Relationships in Data Introductory Concepts of Agile Development Correlation Analysis Creating a Scatter Plot Creating a Bubble Chart Visualizing Bugs Visualizing Production Incidents Interactive Scatter Plots in D3 Adding the Base HTML and JavaScript Loading the Data Adding Interactive Functionality Adding Form Fields Retrieving Form Data Using the Visualization Summary Chapter 9: Visualizing the Balance of Delivery and Quality with Parallel Coordinates What Are Parallel Coordinate Charts? History of Parallel Coordinate Plots Finding Balance Creating a Parallel Coordinate Chart Adding in Effort Brushing Parallel Coordinate Charts with D3 Creating the Base Structure Creating a y-axis for Each Column Drawing the Lines Fading the Lines Creating the Axes Summary Index