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    Instant Heat Maps in R How-to
    Instant Heat Maps in R How-to
    Instant Heat Maps in R How-to
    Ebook137 pages37 minutes

    Instant Heat Maps in R How-to

    By Sebastian Raschka

    ()

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    About this ebook

    In Detail

    R has grown rapidly over the years to become one of the most versatile and valuable tools for data analysis and graphing. One of its many useful features is the heat map representation of numerical data, which is an invaluable tool to discover patterns in data quickly and efficiently.

    Instant Heat Maps in R How-to provides you with practical recipes to create heat maps of all difficulty levels by yourself right from the start. At the end of each recipe, you will find an in-depth analysis that will equip you with everything you need to know to frame the code to your own needs.

    Instant Heat Maps in R will present you with all the different heat map plotting functions that exist in R. You will start by creating simple heat maps before moving on to learn how to add more features to them. While you advance step-by-step through the well-connected recipes, you will find out which tool suits the given situation best. You will learn how to read data from popular file formats and how to format the data to create heat maps as well as the ways to export them for presentation.

    Approach

    Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. Heat Maps in R: How-to is an easy to understand book that starts with a simple heat map and takes you all the way through to advanced heat maps with graphics and data manipulation.

    Who this book is for

    Heat Maps in R How-to is the book for you if you want to make use of this free and open source software to get the most out of your data analysis. You need to have at least some experience in using R and know how to run basic scripts from the command line. However, knowledge of other statistical scripting languages such as Octave, S-Plus, or MATLAB will suffice to follow along with the recipes. You need not be from a statistics background.

    LanguageEnglish
    PublisherPackt Publishing
    Release dateJun 24, 2013
    ISBN9781782165651
    Instant Heat Maps in R How-to

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      Book preview

      Instant Heat Maps in R How-to - Sebastian Raschka

      Table of Contents

      Instant Heat Maps in R How-to

      Credits

      About the Author

      About the Reviewers

      www.PacktPub.com

      Support files, eBooks, discount offers and more

      Why Subscribe?

      Free Access for Packt account holders

      Preface

      What this book covers

      What you need for this book

      Who this book is for

      Conventions

      Reader feedback

      Customer support

      Downloading the example code

      Errata

      Piracy

      Questions

      1. Instant Heat Maps in R How-to

      Creating your first heat map in R (Simple)

      Getting ready

      How to do it...

      How it works...

      There's more...

      More information on dendrograms and clustering

      Reading data from different file formats (Intermediate)

      Getting ready

      How to do it...

      How it works...

      There's more...

      More information on decimal marks

      Customizing heat maps (Intermediate)

      Getting ready

      How to do it...

      How it works...

      Drawing choropleth maps and contour plots (Intermediate)

      Getting ready

      How to do it...

      How it works...

      Exporting for presentation (Simple)

      Getting ready

      How to do it...

      How it works...

      Bringing your data to life (Advanced)

      Getting ready

      How to do it...

      How it works...

      Instant Heat Maps in R How-to

      Instant Heat Maps in R How-to

      Copyright © 2013 Packt Publishing

      All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without the prior written permission of the publisher, except in the case of brief quotations embedded in critical articles or reviews.

      Every effort has been made in the preparation of this book to ensure the accuracy of the information presented. However, the information contained in this book is sold without warranty, either express or implied. Neither the author, nor Packt Publishing, and its dealers and distributors will be held liable for any damages caused or alleged to be caused directly or indirectly by this book.

      Packt Publishing has endeavored to provide trademark information about all of the companies and products mentioned in this book by the appropriate use of capitals. However, Packt Publishing cannot guarantee the accuracy of this information.

      First published: June 2013

      Production Reference: 1180613

      Published by Packt Publishing Ltd.

      Livery Place

      35 Livery Street

      Birmingham B3 2PB, UK.

      ISBN 978-1-78216-564-4

      www.packtpub.com

      Credits

      Author

      Sebastian Raschka

      Reviewers

      John B. Johnston

      Kristopher Opron

      Acquisition Editor

      Martin Bell

      Commissioning Editor

      Yogesh Dalvi

      Technical Editor

      Ankita R. Meshram

      Project Coordinator

      Akash Poojary

      Proofreader

      Paul Hindle

      Production Coordinator

      Nitesh Thakur

      Cover Work

      Nitesh Thakur

      Cover Image

      Aditi Gajjar

      About the Author

      Sebastian Raschka is a PhD student at Michigan State University and is pursuing a doctorate in Biochemistry and Computer Science. He works in the field of protein structure modeling and is focused on the specificity of protein-ligand interactions. His research involves the development of a protein-ligand docking software based on a novel approach, where he combines the fields of machine learning, pattern recognition, and data mining.

      In his free time, Sebastian works on web development and uses JavaScript among other technologies to develop web applications that are used by Bioinformaticians and Computational Biologists.

      About the Reviewers

      John Johnston is the Bioinformatics Domain Specialist for the Institute for Cyber-enabled Research at Michigan State University. He specializes in scientific analysis in a high-performance computing environment, and the development of software for the interpretation of biological data. He is an experienced Linux systems administrator and scientific consultant. He previously worked for 18 years as a Senior Groundwater Scientist for several prominent engineering firms, where he specialized in the delineation and mitigation of environmental contamination and site restoration.

      Kristopher Opron is a PhD student at Michigan State University studying Computational and Mathematical Biology. For his undergraduate research, he worked under Professor Zachary Burton on molecular dynamics simulations of RNA polymerase II. He is currently working on the development of new computational tools for scientists under Professor Guowei Wei.

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