book

R Graphics Cookbook, 2nd Edition

by Winston Chang

November 2018

Beginner to intermediate

441 pages

9h 25m

English

O'Reilly Media, Inc.

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RecipesSoftware and Platform NotesConventions Used in This BookO’ReillyHow to Contact UsAcknowledgments
1.1. Installing a Package1.2. Loading a Package1.3. Upgrading Packages1.4. Loading a Delimited Text Data File1.5. Loading Data from an Excel File1.6. Loading Data from SPSS/SAS/Stata Files1.7. Chaining Functions Together with %>%, the Pipe Operator
2.1. Creating a Scatter Plot2.2. Creating a Line Graph2.3. Creating a Bar Graph2.4. Creating a Histogram2.5. Creating a Box Plot2.6. Plotting a Function Curve
3.1. Making a Basic Bar Graph3.2. Grouping Bars Together3.3. Making a Bar Graph of Counts3.4. Using Colors in a Bar Graph3.5. Coloring Negative and Positive Bars Differently3.6. Adjusting Bar Width and Spacing3.7. Making a Stacked Bar Graph3.8. Making a Proportional Stacked Bar Graph3.9. Adding Labels to a Bar Graph3.10. Making a Cleveland Dot Plot
4.1. Making a Basic Line Graph4.2. Adding Points to a Line Graph4.3. Making a Line Graph with Multiple Lines4.4. Changing the Appearance of Lines4.5. Changing the Appearance of Points4.6. Making a Graph with a Shaded Area4.7. Making a Stacked Area Graph4.8. Making a Proportional Stacked Area Graph4.9. Adding a Confidence Region
5.1. Making a Basic Scatter Plot5.2. Grouping Points Together Using Shapes or Colors5.3. Using Different Point Shapes5.4. Mapping a Continuous Variable to Color or Size5.5. Dealing with Overplotting5.6. Adding Fitted Regression Model Lines5.7. Adding Fitted Lines from an Existing Model5.8. Adding Fitted Lines from Multiple Existing Models5.9. Adding Annotations with Model Coefficients5.10. Adding Marginal Rugs to a Scatter Plot5.11. Labeling Points in a Scatter Plot5.12. Creating a Balloon Plot5.13. Making a Scatter Plot Matrix
6.1. Making a Basic Histogram6.2. Making Multiple Histograms from Grouped Data6.3. Making a Density Curve6.4. Making Multiple Density Curves from Grouped Data6.5. Making a Frequency Polygon6.6. Making a Basic Box Plot6.7. Adding Notches to a Box Plot6.8. Adding Means to a Box Plot6.9. Making a Violin Plot6.10. Making a Dot Plot6.11. Making Multiple Dot Plots for Grouped Data6.12. Making a Density Plot of Two-Dimensional Data
7.1. Adding Text Annotations7.2. Using Mathematical Expressions in Annotations7.3. Adding Lines7.4. Adding Line Segments and Arrows7.5. Adding a Shaded Rectangle7.6. Highlighting an Item7.7. Adding Error Bars7.8. Adding Annotations to Individual Facets
8.1. Swapping X- and Y-Axes8.2. Setting the Range of a Continuous Axis8.3. Reversing a Continuous Axis8.4. Changing the Order of Items on a Categorical Axis8.5. Setting the Scaling Ratio of the X- and Y-Axes8.6. Setting the Positions of Tick Marks8.7. Removing Tick Marks and Labels8.8. Changing the Text of Tick Labels8.9. Changing the Appearance of Tick Labels8.10. Changing the Text of Axis Labels8.11. Removing Axis Labels8.12. Changing the Appearance of Axis Labels8.13. Showing Lines Along the Axes8.14. Using a Logarithmic Axis8.15. Adding Ticks for a Logarithmic Axis8.16. Making a Circular Plot8.17. Using Dates on an Axis8.18. Using Relative Times on an Axis
9.1. Setting the Title of a Graph9.2. Changing the Appearance of Text9.3. Using Themes9.4. Changing the Appearance of Theme Elements9.5. Creating Your Own Themes9.6. Hiding Grid Lines

10.1. Removing the Legend10.2. Changing the Position of a Legend10.3. Changing the Order of Items in a Legend10.4. Reversing the Order of Items in a Legend10.5. Changing a Legend Title10.6. Changing the Appearance of a Legend Title10.7. Removing a Legend Title10.8. Changing the Labels in a Legend10.9. Changing the Appearance of Legend Labels10.10. Using Labels with Multiple Lines of Text
11.1. Splitting Data into Subplots with Facets11.2. Using Facets with Different Axes11.3. Changing the Text of Facet Labels11.4. Changing the Appearance of Facet Labels and Headers
12.1. Setting the Colors of Objects12.2. Representing Variables with Colors12.3. Using a Colorblind-Friendly Palette12.4. Using a Different Palette for a Discrete Variable12.5. Using a Manually Defined Palette for a Discrete Variable12.6. Using a Manually Defined Palette for a Continuous Variable12.7. Coloring a Shaded Region Based on Value
13.1. Making a Correlation Matrix13.2. Plotting a Function13.3. Shading a Subregion Under a Function Curve13.4. Creating a Network Graph13.5. Using Text Labels in a Network Graph13.6. Creating a Heat Map13.7. Creating a Three-Dimensional Scatter Plot13.8. Adding a Prediction Surface to a Three-Dimensional Plot13.9. Saving a Three-Dimensional Plot13.10. Animating a Three-Dimensional Plot13.11. Creating a Dendrogram13.12. Creating a Vector Field13.13. Creating a QQ Plot13.14. Creating a Graph of an Empirical Cumulative Distribution Function13.15. Creating a Mosaic Plot13.16. Creating a Pie Chart13.17. Creating a Map13.18. Creating a Choropleth Map13.19. Making a Map with a Clean Background13.20. Creating a Map from a Shapefile
14.1. Outputting to PDF Vector Files14.2. Outputting to SVG Vector Files14.3. Outputting to WMF Vector Files14.4. Editing a Vector Output File14.5. Outputting to Bitmap (PNG/TIFF) Files14.6. Using Fonts in PDF Files14.7. Using Fonts in Windows Bitmap or Screen Output14.8. Combining Several Plots into the Same Graphic
15.1. Creating a Data Frame15.2. Getting Information About a Data Structure15.3. Adding a Column to a Data Frame15.4. Deleting a Column from a Data Frame15.5. Renaming Columns in a Data Frame15.6. Reordering Columns in a Data Frame15.7. Getting a Subset of a Data Frame15.8. Changing the Order of Factor Levels15.9. Changing the Order of Factor Levels Based on Data Values15.10. Changing the Names of Factor Levels15.11. Removing Unused Levels from a Factor15.12. Changing the Names of Items in a Character Vector15.13. Recoding a Categorical Variable to Another Categorical Variable15.14. Recoding a Continuous Variable to a Categorical Variable15.15. Calculating New Columns from Existing Columns15.16. Calculating New Columns by Groups15.17. Summarizing Data by Groups15.18. Summarizing Data with Standard Errors and Confidence Intervals15.19. Converting Data from Wide to Long15.20. Converting Data from Long to Wide15.21. Converting a Time Series Object to Times and Values
BackgroundSome Terminology and TheoryBuilding a Simple PlotPrintingStatsThemesEnd

Content preview from R Graphics Cookbook, 2nd Edition

Chapter 1. R Basics

This chapter covers the basics: installing and using packages and loading data.

Most of the recipes in this book require the ggplot2, dplyr, and gcookbook packages to be installed on your computer. (The gcookbook package contains the data sets used in some of the examples, but is not necessary for doing your real work.) If you want to get started quickly, run:

install.packages("tidyverse")
install.packages("gcookbook")

Then, in each R session, before running the examples in this book, you can load them with:

library(tidyverse)
library(gcookbook)

Running library(tidyverse) will load ggplot2, dplyr, and a number of other packages. If you want to keep your R session more streamlined and load only the packages that are strictly needed, you can load the ggplot2 and dplyr packages individually:

library(ggplot2)
library(dplyr)
library(gcookbook)

Note

If you want a deeper understanding of how ggplot2 works, see Appendix A, which explains the concepts behind ggplot2.

Packages in R are collections of functions and/or data that are bundled up for easy distribution, and installing a package will extend the functionality of R on your computer. If an R user creates a package and thinks that it might be useful for others, that user can distribute it through a package repository. The primary repository for distributing R packages is called CRAN (the Comprehensive R Archive Network), but there are others, such as Bioconductor, which specializes in packages related to genomic ...