The Data Analysis, Data Transformation, and Modelling for Visualisation chapters have been removed so that the book can focus on visualisation. If you’re looking for general advice on doing data science in R, I recommend R for Data Science.
The Toolbox chapter has been expanded into six chapters that cover practical applications of layers. This includes more material on maps and annotations, and a new chapter that discusses how to arrange multiple plots on one page.
Similarly, the old Scales, Axes, and Legends chapter has been split into into four chapters. The first three cover the practical combination of scales and guides for the most common scale types, and the final chapter focusses on the underlying theory.
The old Positioning chapter has been split into new Coordinate Systems and Faceting chapters, giving more room for details on these important topics.
New chapters describe more about the internals of ggplot2, and how you can extend it in your own package.