Done. 🏁

ggplot.Rnw

@@ -9,15 +9,11 @@
 \setcounter{secnumdepth}{-1}
 \usetheme{Amsterdam}
 % --------------------------------------------------------------
+% Setting up some knitr options
 <<setup, include=FALSE>>=
 opts_chunk$set(cache=TRUE, message=FALSE)
 # smaller font size for chunks
 opts_chunk$set(size = 'footnotesize')
-@
-
-% --------------------------------------------------------------
-% Setting up some knitr options
-<<echo=FALSE>>=
 options(width = 60)
 @
 
@@ -30,7 +26,7 @@ options(width = 60)
 \begin{frame}[fragile]
 \frametitle{Some housekeeping}
 Install some packages
-<<some_data22, tidy=FALSE, echo=TRUE, eval=FALSE>>=
+<<installation, tidy=FALSE, echo=TRUE, eval=FALSE>>=
 install.packages("ggplot2", dependencies = TRUE)
 @
 \end{frame}
@@ -152,7 +148,7 @@ myplot + geom_point()
 \begin{frame}[fragile]
 \frametitle{Increase the size of points}
 <<first_plot_size , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
-ggplot(data = iris, aes(x= Sepal.Length, y= Sepal.Width)) +
+ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width)) +
 geom_point(size = 3)
 @
 \end{frame}
@@ -291,7 +287,7 @@ geom_bar(stat = "identity")
 % --------------------------------------------------------------
 \begin{frame}[fragile]
 <<bartwo , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
-df  <- melt(iris, id.vars="Species")
+df  <- melt(iris, id.vars = "Species")
 ggplot(df, aes(Species, value, fill = variable)) +
 geom_bar(stat = "identity")
 @
@@ -413,7 +409,7 @@ display.brewer.all()
 \begin{frame}[fragile]
 \frametitle{Using a color brewer palette}
 <<barcolors, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
-df  <- melt(iris, id.vars="Species")
+df  <- melt(iris, id.vars = "Species")
 ggplot(df, aes(Species, value, fill = variable)) +
 geom_bar(stat = "identity", position = "dodge") +
 scale_fill_brewer(palette = "Set1")
@@ -592,8 +588,8 @@ scale_linetype(), scale_shape_manual()
 library(MASS)
 ggplot(birthwt, aes(factor(race), bwt)) +
 geom_boxplot(width = .2) +
-scale_y_continuous(labels = (paste0(1:4, " K")),
-breaks=seq(1000, 4000, by = 1000))
+scale_y_continuous(labels = (paste0(1:4, " Kg")),
+breaks = seq(1000, 4000, by = 1000))
 @
 \end{frame}
 
@@ -608,8 +604,8 @@ geom_point(size = 4, shape = 16) +
 facet_grid(. ~Species)
 # Now add a scale
 dd +
-scale_y_continuous(breaks=seq(2, 8,by = 1),
-labels=paste0(2:8, " cm"))
+scale_y_continuous(breaks = seq(2, 8, by = 1),
+labels = paste0(2:8, " cm"))
 @
 \end{frame}
 
@@ -629,18 +625,19 @@ ggsave('~/path/to/figure/filename.png')
 @
 \item If your plot is assigned to an object
 <<pub1, eval = FALSE, out.width='.75\\linewidth'>>=
-ggsave(plot1, '~/path/to/figure/filename.png')
+ggsave(plot1, file = "~/path/to/figure/filename.png")
 @
 
 \item Specify a size
-<<pub2, eval = FALSE, out.width='.75\\linewidth'>>=
-ggsave("/path/to/figure/filename.png", width = 6, height =4)
+<<pub2, eval = FALSE, out.width='.75\\linewidth', tidy = FALSE>>=
+ggsave(file = "/path/to/figure/filename.png", width = 6,
+height =4)
 @
 \item or any format (pdf, png, eps, svg, jpg)
 <<pub3, eval = FALSE, out.width=".75\\linesewidth">>=
-ggsave("/path/to/figure/filename.eps")
-ggsave("/path/to/figure/filename.jpg")
-ggsave("/path/to/figure/filename.pdf")
+ggsave(file = "/path/to/figure/filename.eps")
+ggsave(file = "/path/to/figure/filename.jpg")
+ggsave(file = "/path/to/figure/filename.pdf")
 @
 \end{itemize}
 \end{frame}

ggplot.tex

@@ -62,10 +62,6 @@
 \usepackage{url}
 \setcounter{secnumdepth}{-1}
 \usetheme{Amsterdam}
-% --------------------------------------------------------------
-
-
-
 % --------------------------------------------------------------
 % Setting up some knitr options
 
@@ -236,7 +232,7 @@ \section*{Assembling your first ggplot}
 \begin{knitrout}\footnotesize
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{alltt}
-\hlfunctioncall{ggplot}(data = iris, \hlfunctioncall{aes}(x= Sepal.Length, y= Sepal.Width)) +
+\hlfunctioncall{ggplot}(data = iris, \hlfunctioncall{aes}(x = Sepal.Length, y = Sepal.Width)) +
 \hlfunctioncall{geom_point}(size = 3)
 \end{alltt}
 \end{kframe}
@@ -443,7 +439,7 @@ \section*{Bar plots}
 \begin{knitrout}\footnotesize
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{alltt}
-df  <- \hlfunctioncall{melt}(iris, id.vars=\hlstring{"Species"})
+df  <- \hlfunctioncall{melt}(iris, id.vars = \hlstring{"Species"})
 \hlfunctioncall{ggplot}(df, \hlfunctioncall{aes}(Species, value, fill = variable)) +
 \hlfunctioncall{geom_bar}(stat = \hlstring{"identity"})
 \end{alltt}
@@ -629,7 +625,7 @@ \section*{Mapping Variables to colors}
 \begin{knitrout}\footnotesize
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{alltt}
-df  <- \hlfunctioncall{melt}(iris, id.vars=\hlstring{"Species"})
+df  <- \hlfunctioncall{melt}(iris, id.vars = \hlstring{"Species"})
 \hlfunctioncall{ggplot}(df, \hlfunctioncall{aes}(Species, value, fill = variable)) +
 \hlfunctioncall{geom_bar}(stat = \hlstring{"identity"}, position = \hlstring{"dodge"}) +
 \hlfunctioncall{scale_fill_brewer}(palette = \hlstring{"Set1"})
@@ -879,8 +875,8 @@ \section*{Scales}
 \hlfunctioncall{library}(MASS)
 \hlfunctioncall{ggplot}(birthwt, \hlfunctioncall{aes}(\hlfunctioncall{factor}(race), bwt)) +
 \hlfunctioncall{geom_boxplot}(width = .2) +
-\hlfunctioncall{scale_y_continuous}(labels = (\hlfunctioncall{paste0}(1:4, \hlstring{" K"})),
-breaks=\hlfunctioncall{seq}(1000, 4000, by = 1000))
+\hlfunctioncall{scale_y_continuous}(labels = (\hlfunctioncall{paste0}(1:4, \hlstring{" Kg"})),
+breaks = \hlfunctioncall{seq}(1000, 4000, by = 1000))
 \end{alltt}
 \end{kframe}
 \includegraphics[width=.75\linewidth]{figure/boxplots3_} 
@@ -902,8 +898,8 @@ \section*{Scales}
 \hlfunctioncall{facet_grid}(. ~Species)
 \hlcomment{# Now add a scale}
 dd +
-\hlfunctioncall{scale_y_continuous}(breaks=\hlfunctioncall{seq}(2, 8,by = 1),
-labels=\hlfunctioncall{paste0}(2:8, \hlstring{" cm"}))
+\hlfunctioncall{scale_y_continuous}(breaks = \hlfunctioncall{seq}(2, 8, by = 1),
+labels = \hlfunctioncall{paste0}(2:8, \hlstring{" cm"}))
 \end{alltt}
 \end{kframe}
 \end{knitrout}
@@ -933,7 +929,7 @@ \section*{Publication quality figures}
 \begin{knitrout}\footnotesize
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{alltt}
-\hlfunctioncall{ggsave}(plot1, \hlstring{"~/path/to/figure/filename.png"})
+\hlfunctioncall{ggsave}(plot1, file = \hlstring{"~/path/to/figure/filename.png"})
 \end{alltt}
 \end{kframe}
 \end{knitrout}
@@ -943,7 +939,8 @@ \section*{Publication quality figures}
 \begin{knitrout}\footnotesize
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{alltt}
-\hlfunctioncall{ggsave}(\hlstring{"/path/to/figure/filename.png"}, width = 6, height = 4)
+\hlfunctioncall{ggsave}(file = \hlstring{"/path/to/figure/filename.png"}, width = 6,
+height =4)
 \end{alltt}
 \end{kframe}
 \end{knitrout}
@@ -952,9 +949,9 @@ \section*{Publication quality figures}
 \begin{knitrout}\footnotesize
 \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 \begin{alltt}
-\hlfunctioncall{ggsave}(\hlstring{"/path/to/figure/filename.eps"})
-\hlfunctioncall{ggsave}(\hlstring{"/path/to/figure/filename.jpg"})
-\hlfunctioncall{ggsave}(\hlstring{"/path/to/figure/filename.pdf"})
+\hlfunctioncall{ggsave}(file = \hlstring{"/path/to/figure/filename.eps"})
+\hlfunctioncall{ggsave}(file = \hlstring{"/path/to/figure/filename.jpg"})
+\hlfunctioncall{ggsave}(file = \hlstring{"/path/to/figure/filename.pdf"})
 \end{alltt}
 \end{kframe}
 \end{knitrout}