First commit after splitting the original R appendixes into a separat…

…e book.

R.more.plotting.Rnw

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+% !Rnw root = appendix.main.Rnw
+
+<<echo=FALSE, include=FALSE>>=
+opts_chunk$set(opts_fig_wide)
+opts_knit$set(concordance=TRUE)
+@
+
+\chapter[Plots with ggpplot, ggrepel and ggpmisc]{Plots with \ggplot, \ggrepel and \ggpmisc}\label{chap:R:plotting}
+
+\section{Packages used in this chapter}
+
+For executing the examples listed in this chapter you need first to load the following packages from the library:
+
+<<message=FALSE>>=
+library(ggplot2)
+library(ggrepel)
+library(ggpmisc)
+@
+
+We set a font larger size than the default
+<<>>=
+theme_set(theme_grey(16))
+@
+<<echo=FALSE,include=FALSE>>=
+opts_chunk$set(opts_fig_narrow)
+@
+
+<<eval=eval_diag, include=eval_diag, echo=eval_diag, cache=FALSE>>=
+opts_knit$get()
+search()
+getwd()
+@
+
+\section[ggpmisc]{\ggpmisc}
+
+\subsection{New stats}
+
+Package \ggpmisc provides new stats: \code{stat\_peaks()}, \code{stat\_valleys()}, and \code{stat\_poly\_eq()}. Peaks and valleys are local (or global) maxima and minima. These stats return the $x$ and $y$ values at the peaks or valleys plus suitable labels, and default aesthetics that make easy their use with several different geoms, including \code{geom\_point}, \code{geom\_text}, \code{geom\_label}, \code{geom\_vline}, \code{geom\_hline} and \code{geom\_rug}, and also with geoms defined by package \ggrepel. Some examples follow.
+
+\subsection{Peaks and valleys}
+<<>>=
+lynx.df <- data.frame(year = as.numeric(time(lynx)), lynx = as.matrix(lynx))
+@
+
+<<>>=
+ggplot(lynx.df, aes(year, lynx)) + geom_line() +
+  stat_peaks(colour = "red") +
+  stat_peaks(geom = "text", colour = "red", 
+             vjust = -0.5, x.label.fmt = "%4.0f") +
+  stat_valleys(colour = "blue") +
+  stat_valleys(geom = "text", colour = "blue", 
+               vjust = 1.5, x.label.fmt = "%4.0f") +
+  ylim(-100, 7300)
+@
+
+<<>>=
+ggplot(lynx.df, aes(year, lynx)) + geom_line() +
+  stat_peaks(colour = "red") +
+  stat_peaks(geom = "rug", colour = "red") +
+  stat_peaks(geom = "text", colour = "red", 
+             vjust = -0.5, x.label.fmt = "%4.0f") +
+  ylim(NA, 7300)
+
+@
+
+<<>>=
+ggplot(lynx.df, aes(year, lynx)) + geom_line() +
+  stat_peaks(colour = "red") +
+  stat_peaks(geom = "rug", colour = "red") +
+  stat_valleys(colour = "blue") +
+  stat_valleys(geom = "rug", colour = "blue")
+@
+
+<<>>=
+ggplot(lynx.df, aes(year, lynx)) + geom_line() +
+  stat_peaks(colour = "red") +
+  stat_peaks(geom = "rug", colour = "red") +
+  stat_peaks(geom = "text", colour = "red",
+             hjust = -0.1, label.fmt = "%4.0f", 
+             angle = 90, size = rel(2),
+             aes(label = paste(..y.label.., 
+                               "skins in year", ..x.label..))) +
+  stat_valleys(colour = "blue") +
+  stat_valleys(geom = "rug", colour = "blue") +
+  stat_valleys(geom = "text", colour = "blue",
+             hjust = -0.1, vjust = 1, label.fmt = "%4.0f", 
+             angle = 90, size = rel(2),
+             aes(label = paste(..y.label.., 
+                               "skins in year", ..x.label..))) +
+  ylim(NA, 10000)
+@
+
+Of course, if one finds use for it, the peaks and/or valleys can be plotted on their own.
+
+<<>>=
+ggplot(lynx.df, aes(year, lynx)) + 
+  stat_peaks(geom = "line") + stat_valleys(geom = "line")
+@
+\subsection{Learning and/or debugging}
+
+A very simple stat named \code{stat\_debug()} can save the work of adding print statements to the code of stats to get information about what data is being passed to the \code{compute\_group()} function. Because the code of this function is stored in a \code{ggproto} object, at the moment it is impossible to directly set breakpoints in it. This stat may also help users diagnose problems with the mapping of aesthetics in their code or just get a better idea of how the internals of \ggplot work.
+
+<<>>=
+ggplot(lynx.df, aes(year, lynx)) + geom_line() +
+  stat_debug(alpha = 0.8)
+@
+
+<<>>=
+lynx.df$century <- ifelse(lynx.df$year >= 1900, "XX", "XIX") 
+ggplot(lynx.df, aes(year, lynx, color = century)) + 
+  geom_line() +
+  stat_debug(alpha = 0.8, size = rel(2.5))
+@
+
+\section[ggrepel]{\ggrepel}
+
+\subsection{New geoms}
+
+Package \ggrepel provides two new geoms: \code{geom\_text\_repel} and \code{geom\_label\_repel}. They are used similarly to \code{geom\_text} and \code{geom\_label} but the text or labels ``repel'' each other so that they rarely overlap unless the plot is very crowded. 
+
+
+<<>>=
+try(detach(package:ggpmisc))
+try(detach(package:ggrepel))
+try(detach(package:ggplot2))
+@
+