├── .gitignore
├── README.md
├── beamerthemeAmsterdam.sty
├── climate.csv
├── ggplot.R
├── ggplot.Rnw
├── ggplot.pdf
├── ggplot.tex
├── images
    ├── chang_book.png
    ├── color_palette.png
    ├── color_schemes.png
    ├── git_repo.png
    └── hadley.png
├── make.sh
└── slides.png


/.gitignore:
--------------------------------------------------------------------------------
 1 | *.log
 2 | *.nav
 3 | *.out
 4 | *.snm
 5 | *.tex
 6 | *.toc
 7 | *.vrb
 8 | *.aux
 9 | *.sh
10 | .DS_Store
11 | figure/
12 | local.R
13 | cache/*
14 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | # Introduction to ggplot2
 2 | 
 3 | Author: [Karthik Ram](mailto:karthik.ram+ggplot2@gmail.com)
 4 | 
 5 | Here are my [slides](https://github.com/karthikram/ggplot-lecture/blob/master/ggplot.pdf?raw=true) for the Spring 2013 R seminar in Integrative Biology at UC Berkeley. The source file is `ggplot.Rnw`. Feel free to modify and reuse as necessary.
 6 | 
 7 | [![slides](slides.png)](https://github.com/karthikram/ggplot-lecture/blob/master/ggplot.pdf?raw=true)
 8 | 
 9 | To generate the pdf presentation locally:
10 | 
11 | ```r
12 | knitr('ggplot.Rnw')
13 | system("pdflatex ggplot.tex")
14 | ```
15 | 
16 | * [R code from the deck](https://github.com/karthikram/ggplot-lecture/blob/master/ggplot.R)
17 | 
18 | ## Suggested readings
19 | * [Elegant graphics for data analysis](http://www.amazon.com/ggplot2-Ele gant-Graphics-Data-Analysis/dp/0387981403/)  
20 | *  [R Graphics Cookbook](http://www.amazon.com/R-Graphics-Cookbook-Winston-Chang/dp/1449316956)
21 | 
22 | # License  
23 | <a rel="license" href="http://creativecommons.org/licenses/by/2.0/">Creative Commons Attribution 2.0 Generic License</a>.
24 | 


--------------------------------------------------------------------------------
/beamerthemeAmsterdam.sty:
--------------------------------------------------------------------------------
 1 | \DeclareOptionBeamer{compress}{\beamer@compresstrue}
 2 | \ProcessOptionsBeamer
 3 | 
 4 | \mode<presentation>
 5 | 
 6 | \useoutertheme[footline=authortitle]{miniframes}
 7 | \useinnertheme{circles}
 8 | \usecolortheme{whale}
 9 | \usecolortheme{orchid}
10 | 
11 | \definecolor{beamer@blendedblue}{rgb}{0.137,0.466,0.741}
12 | 
13 | \setbeamercolor{structure}{fg=beamer@blendedblue}
14 | \setbeamercolor{titlelike}{parent=structure}
15 | \setbeamercolor{frametitle}{fg=black}
16 | \setbeamercolor{title}{fg=black}
17 | \setbeamercolor{item}{fg=black}
18 | 
19 | \mode
20 | <all>
21 | 


--------------------------------------------------------------------------------
/climate.csv:
--------------------------------------------------------------------------------
  1 | "","Source","Year","Anomaly1y","Anomaly5y","Anomaly10y","Unc10y"
  2 | "102","Berkeley",1901,NA,NA,-0.162,0.109
  3 | "103","Berkeley",1902,NA,NA,-0.177,0.108
  4 | "104","Berkeley",1903,NA,NA,-0.199,0.104
  5 | "105","Berkeley",1904,NA,NA,-0.223,0.105
  6 | "106","Berkeley",1905,NA,NA,-0.241,0.107
  7 | "107","Berkeley",1906,NA,NA,-0.294,0.106
  8 | "108","Berkeley",1907,NA,NA,-0.312,0.105
  9 | "109","Berkeley",1908,NA,NA,-0.328,0.103
 10 | "110","Berkeley",1909,NA,NA,-0.281,0.101
 11 | "111","Berkeley",1910,NA,NA,-0.247,0.099
 12 | "112","Berkeley",1911,NA,NA,-0.243,0.097
 13 | "113","Berkeley",1912,NA,NA,-0.257,0.1
 14 | "114","Berkeley",1913,NA,NA,-0.268,0.1
 15 | "115","Berkeley",1914,NA,NA,-0.257,0.097
 16 | "116","Berkeley",1915,NA,NA,-0.249,0.095
 17 | "117","Berkeley",1916,NA,NA,-0.214,0.096
 18 | "118","Berkeley",1917,NA,NA,-0.201,0.096
 19 | "119","Berkeley",1918,NA,NA,-0.176,0.096
 20 | "120","Berkeley",1919,NA,NA,-0.182,0.097
 21 | "121","Berkeley",1920,NA,NA,-0.193,0.097
 22 | "122","Berkeley",1921,NA,NA,-0.167,0.098
 23 | "123","Berkeley",1922,NA,NA,-0.128,0.096
 24 | "124","Berkeley",1923,NA,NA,-0.075,0.097
 25 | "125","Berkeley",1924,NA,NA,-0.064,0.098
 26 | "126","Berkeley",1925,NA,NA,-0.065,0.1
 27 | "127","Berkeley",1926,NA,NA,-0.05,0.1
 28 | "128","Berkeley",1927,NA,NA,-0.02,0.099
 29 | "129","Berkeley",1928,NA,NA,-0.018,0.099
 30 | "130","Berkeley",1929,NA,NA,-0.026,0.1
 31 | "131","Berkeley",1930,NA,NA,-0.014,0.101
 32 | "132","Berkeley",1931,NA,NA,-0.047,0.098
 33 | "133","Berkeley",1932,NA,NA,-0.035,0.096
 34 | "134","Berkeley",1933,NA,NA,-0.017,0.093
 35 | "135","Berkeley",1934,NA,NA,0.02,0.092
 36 | "136","Berkeley",1935,NA,NA,0.053,0.089
 37 | "137","Berkeley",1936,NA,NA,0.063,0.085
 38 | "138","Berkeley",1937,NA,NA,0.048,0.081
 39 | "139","Berkeley",1938,NA,NA,0.073,0.079
 40 | "140","Berkeley",1939,NA,NA,0.113,0.076
 41 | "141","Berkeley",1940,NA,NA,0.113,0.072
 42 | "142","Berkeley",1941,NA,NA,0.134,0.071
 43 | "143","Berkeley",1942,NA,NA,0.134,0.069
 44 | "144","Berkeley",1943,NA,NA,0.127,0.07
 45 | "145","Berkeley",1944,NA,NA,0.111,0.068
 46 | "146","Berkeley",1945,NA,NA,0.072,0.066
 47 | "147","Berkeley",1946,NA,NA,0.035,0.066
 48 | "148","Berkeley",1947,NA,NA,0.042,0.064
 49 | "149","Berkeley",1948,NA,NA,0.045,0.063
 50 | "150","Berkeley",1949,NA,NA,0.013,0.062
 51 | "151","Berkeley",1950,NA,NA,0.01,0.058
 52 | "152","Berkeley",1951,NA,NA,-0.017,0.054
 53 | "153","Berkeley",1952,NA,NA,-0.04,0.047
 54 | "154","Berkeley",1953,NA,NA,-0.04,0.043
 55 | "155","Berkeley",1954,NA,NA,-0.032,0.038
 56 | "156","Berkeley",1955,NA,NA,-0.022,0.035
 57 | "157","Berkeley",1956,NA,NA,0.012,0.031
 58 | "158","Berkeley",1957,NA,NA,0.007,0.028
 59 | "159","Berkeley",1958,NA,NA,0.002,0.027
 60 | "160","Berkeley",1959,NA,NA,0.002,0.026
 61 | "161","Berkeley",1960,NA,NA,-0.019,0.026
 62 | "162","Berkeley",1961,NA,NA,-0.001,0.021
 63 | "163","Berkeley",1962,NA,NA,0.017,0.018
 64 | "164","Berkeley",1963,NA,NA,0.004,0.016
 65 | "165","Berkeley",1964,NA,NA,-0.028,0.018
 66 | "166","Berkeley",1965,NA,NA,-0.006,0.017
 67 | "167","Berkeley",1966,NA,NA,-0.024,0.017
 68 | "168","Berkeley",1967,NA,NA,-0.041,0.019
 69 | "169","Berkeley",1968,NA,NA,-0.025,0.02
 70 | "170","Berkeley",1969,NA,NA,-0.019,0.024
 71 | "171","Berkeley",1970,NA,NA,0.01,0.026
 72 | "172","Berkeley",1971,NA,NA,0.007,0.022
 73 | "173","Berkeley",1972,NA,NA,0.015,0.015
 74 | "174","Berkeley",1973,NA,NA,0.028,0.012
 75 | "175","Berkeley",1974,NA,NA,0.049,0.014
 76 | "176","Berkeley",1975,NA,NA,0.068,0.012
 77 | "177","Berkeley",1976,NA,NA,0.128,0.011
 78 | "178","Berkeley",1977,NA,NA,0.158,0.012
 79 | "179","Berkeley",1978,NA,NA,0.167,0.013
 80 | "180","Berkeley",1979,NA,NA,0.193,0.012
 81 | "181","Berkeley",1980,NA,NA,0.186,0.016
 82 | "182","Berkeley",1981,NA,NA,0.217,0.016
 83 | "183","Berkeley",1982,NA,NA,0.235,0.014
 84 | "184","Berkeley",1983,NA,NA,0.27,0.014
 85 | "185","Berkeley",1984,NA,NA,0.318,0.014
 86 | "186","Berkeley",1985,NA,NA,0.344,0.013
 87 | "187","Berkeley",1986,NA,NA,0.352,0.012
 88 | "188","Berkeley",1987,NA,NA,0.38,0.011
 89 | "189","Berkeley",1988,NA,NA,0.37,0.013
 90 | "190","Berkeley",1989,NA,NA,0.366,0.017
 91 | "191","Berkeley",1990,NA,NA,0.433,0.019
 92 | "192","Berkeley",1991,NA,NA,0.467,0.018
 93 | "193","Berkeley",1992,NA,NA,0.496,0.017
 94 | "194","Berkeley",1993,NA,NA,0.526,0.019
 95 | "195","Berkeley",1994,NA,NA,0.554,0.02
 96 | "196","Berkeley",1995,NA,NA,0.563,0.019
 97 | "197","Berkeley",1996,NA,NA,0.565,0.022
 98 | "198","Berkeley",1997,NA,NA,0.618,0.022
 99 | "199","Berkeley",1998,NA,NA,0.68,0.023
100 | "200","Berkeley",1999,NA,NA,0.734,0.025
101 | "201","Berkeley",2000,NA,NA,0.748,0.026
102 | "202","Berkeley",2001,NA,NA,0.793,0.027
103 | "203","Berkeley",2002,NA,NA,0.856,0.028
104 | "204","Berkeley",2003,NA,NA,0.869,0.028
105 | "205","Berkeley",2004,NA,NA,0.884,0.029
106 | 


--------------------------------------------------------------------------------
/ggplot.R:
--------------------------------------------------------------------------------
  1 | 
  2 | 
  3 | opts_chunk$set(cache=TRUE, message=FALSE)
  4 | # smaller font size for chunks
  5 | opts_chunk$set(size = 'footnotesize')
  6 | options(width = 60)
  7 | 
  8 | 
  9 | 
 10 | ## install.packages("ggplot2", dependencies = TRUE)
 11 | 
 12 | 
 13 | 
 14 | head(iris)
 15 | 
 16 | 
 17 | 
 18 | ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width)) +
 19 | geom_point()
 20 | 
 21 | 
 22 | 
 23 | ## ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width))
 24 | ##  + geom_point()
 25 | ## myplot <- ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width))
 26 | ## myplot + geom_point()
 27 | 
 28 | 
 29 | 
 30 | ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width)) +
 31 | geom_point(size = 3)
 32 | 
 33 | 
 34 | 
 35 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
 36 | geom_point(size = 3)
 37 | 
 38 | 
 39 | 
 40 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
 41 | geom_point(aes(shape = Species), size = 3)
 42 | 
 43 | 
 44 | 
 45 | ## # Make a small sample of the diamonds dataset
 46 | ## d2 <- diamonds[sample(1:dim(diamonds)[1], 1000), ]
 47 | 
 48 | # Efficient and more readable random sample
 49 | # d2 <- diamonds[sample(nrow(diamonds), 1000), ]
 50 | 
 51 | # Robust and more readable random sample
 52 | # d2 <- diamonds[sample(1:nrow(diamonds), 1000, replace = FALSE), ]
 53 | 
 54 | 
 55 | d2 <- diamonds[sample(1:dim(diamonds)[1], 1000), ]
 56 | ggplot(d2, aes(carat, price, color = color)) + geom_point() + theme_gray()
 57 | 
 58 | 
 59 | 
 60 | library(MASS)
 61 | ggplot(birthwt, aes(factor(race), bwt)) + geom_boxplot()
 62 | 
 63 | 
 64 | 
 65 | h <- ggplot(faithful, aes(x = waiting))
 66 | h + geom_histogram(binwidth = 30, colour = "black")
 67 | 
 68 | 
 69 | 
 70 | h <- ggplot(faithful, aes(x = waiting))
 71 | h + geom_histogram(binwidth = 8, fill = "steelblue",
 72 | colour = "black")
 73 | 
 74 | 
 75 | 
 76 | setwd('~/Github/ggplot2-lecture/')
 77 | 
 78 | 
 79 | 
 80 | climate <- read.csv("climate.csv", header = T)
 81 | ggplot(climate, aes(Year, Anomaly10y)) +
 82 | geom_line()
 83 | 
 84 | 
 85 | 
 86 | ggplot(climate, aes(Year, Anomaly10y)) +
 87 | geom_ribbon(aes(ymin = Anomaly10y - Unc10y,
 88 | ymax = Anomaly10y + Unc10y),
 89 | fill = "blue", alpha = .1) +
 90 | geom_line(color = "steelblue")
 91 | 
 92 | 
 93 | 
 94 | cplot <- ggplot(climate, aes(Year, Anomaly10y))
 95 | cplot <- cplot + geom_line(size = 0.7, color = "black")
 96 | cplot <- cplot + geom_line(aes(Year, Anomaly10y + Unc10y), linetype = "dashed", size = 0.7, color = "red")
 97 | cplot <- cplot + geom_line(aes(Year, Anomaly10y - Unc10y), linetype = "dashed", size = 0.7, color = "red")
 98 | cplot + theme_gray()
 99 | 
100 | 
101 | 
102 | ggplot(iris, aes(Species, Sepal.Length)) +
103 | geom_bar(stat = "identity")
104 | 
105 | 
106 | 
107 | df  <- melt(iris, id.vars = "Species")
108 | ggplot(df, aes(Species, value, fill = variable)) +
109 | geom_bar(stat = "identity")
110 | 
111 | 
112 | 
113 | iris[1:2, ]
114 | df  <- melt(iris, id.vars = "Species")
115 | df[1:2, ]
116 | 
117 | 
118 | 
119 | ggplot(df, aes(Species, value, fill = variable)) +
120 | geom_bar(stat = "identity", position = "dodge")
121 | 
122 | 
123 | 
124 | ggplot(d2, aes(clarity, fill = cut)) +
125 | geom_bar(position = "dodge",stat = "bin") + theme_gray()
126 | 
127 | 
128 | 
129 | clim <- read.csv('climate.csv', header = TRUE)
130 | clim$sign <- ifelse(clim$Anomaly10y<0, FALSE, TRUE)
131 | # or as simple as
132 | # clim$sign <- clim$Anomaly10y < 0
133 | ggplot(clim, aes(Year, Anomaly10y)) + geom_bar(stat = "identity", aes(fill = sign)) + theme_gray()
134 | 
135 | 
136 | 
137 | ggplot(faithful, aes(waiting)) + geom_density()
138 | 
139 | 
140 | 
141 | ggplot(faithful, aes(waiting)) +
142 | geom_density(fill = "blue", alpha = 0.1)
143 | 
144 | 
145 | 
146 | ggplot(faithful, aes(waiting)) +
147 | geom_line(stat = "density")
148 | 
149 | 
150 | 
151 | ## aes(color = variable)
152 | ## aes(color = "black")
153 | ## # Or add it as a scale
154 | ## scale_fill_manual(values = c("color1", "color2"))
155 | 
156 | 
157 | 
158 | ## library(RColorBrewer)
159 | ## display.brewer.all()
160 | 
161 | 
162 | 
163 | df  <- melt(iris, id.vars = "Species")
164 | ggplot(df, aes(Species, value, fill = variable)) +
165 | geom_bar(stat = "identity", position = "dodge") +
166 | scale_fill_brewer(palette = "Set1")
167 | 
168 | 
169 | 
170 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
171 | geom_point() +
172 | facet_grid(Species ~ .) +
173 | scale_color_manual(values = c("red", "green", "blue"))
174 | 
175 | 
176 | 
177 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
178 | geom_point() +
179 | facet_grid(Species ~ .)
180 | 
181 | 
182 | 
183 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
184 | geom_point() +
185 | facet_grid(. ~ Species)
186 | 
187 | 
188 | 
189 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
190 | geom_point() +
191 | facet_wrap( ~ Species)
192 | 
193 | 
194 | 
195 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
196 | geom_point(aes(shape = Species), size = 3) +
197 | geom_smooth(method = "lm")
198 | 
199 | 
200 | 
201 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
202 | geom_point(aes(shape = Species), size = 3) +
203 | geom_smooth(method = "lm") +
204 | facet_grid(. ~ Species)
205 | 
206 | 
207 | 
208 | ## + theme()
209 | ## # see ?theme() for more options
210 | 
211 | 
212 | 
213 | ## ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
214 | ## geom_point(size = 1.2, shape = 16) +
215 | ## facet_wrap( ~ Species) +
216 | ## theme(legend.key = element_rect(fill = NA),
217 | ## legend.position = "bottom",
218 | ## strip.background = element_rect(fill = NA),
219 | ## axis.title.y = element_text(angle = 0))
220 | 
221 | 
222 | 
223 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
224 | geom_point(size = 1.2, shape = 16) +
225 | facet_wrap( ~ Species) +
226 | theme(legend.key = element_rect(fill = NA),
227 | legend.position = "bottom",
228 | strip.background = element_rect(fill = NA),
229 | axis.title.y = element_text(angle = 0))
230 | 
231 | 
232 | 
233 | ## install.packages('ggthemes')
234 | ## library(ggthemes)
235 | ## # Then add one of these themes to your plot
236 | ##  + theme_stata()
237 | ##  + theme_excel()
238 | ##  + theme_wsj()
239 | ##  + theme_solarized()
240 | 
241 | 
242 | 
243 | ## my_custom_plot <- function(df, title = "", ...) {
244 | ##     ggplot(df, ...) +
245 | ##     ggtitle(title) +
246 | ##     whatever geoms() +
247 | ##     theme(...)
248 | ## }
249 | 
250 | 
251 | 
252 | ## plot1 <- my_custom_plot(dataset1, title = "Figure 1")
253 | 
254 | 
255 | 
256 | ## scale_fill_discrete(), scale_colour_discrete()
257 | ## scale_fill_hue(), scale_color_hue()
258 | ## scale_fill_manual(),  scale_color_manual()
259 | ## scale_fill_brewer(), scale_color_brewer()
260 | ## scale_linetype(), scale_shape_manual()
261 | 
262 | 
263 | 
264 | library(MASS)
265 | ggplot(birthwt, aes(factor(race), bwt)) +
266 | geom_boxplot(width = .2) +
267 | scale_y_continuous(labels = (paste0(1:4, " Kg")),
268 | breaks = seq(1000, 4000, by = 1000))
269 | 
270 | 
271 | 
272 | ## # Assign the plot to an object
273 | ## dd <- ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
274 | ## geom_point(size = 4, shape = 16) +
275 | ## facet_grid(. ~Species)
276 | ## # Now add a scale
277 | ## dd +
278 | ## scale_y_continuous(breaks = seq(2, 8, by = 1),
279 | ## labels = paste0(2:8, " cm"))
280 | 
281 | 
282 | 
283 | h + geom_histogram( aes(fill = ..count..), color="black") +
284 | scale_fill_gradient(low="green", high="red")
285 | 
286 | 
287 | 
288 | ## ggsave('~/path/to/figure/filename.png')
289 | 
290 | 
291 | 
292 | ## ggsave(plot1, file = "~/path/to/figure/filename.png")
293 | 
294 | 
295 | 
296 | ## ggsave(file = "/path/to/figure/filename.png", width = 6,
297 | ## height =4)
298 | 
299 | 
300 | 
301 | ## ggsave(file = "/path/to/figure/filename.eps")
302 | ## ggsave(file = "/path/to/figure/filename.jpg")
303 | ## ggsave(file = "/path/to/figure/filename.pdf")
304 | 
305 | 
306 | 


--------------------------------------------------------------------------------
/ggplot.Rnw:
--------------------------------------------------------------------------------
  1 | % Introduction to ggplot2
  2 | % Author: Karthik Ram, karthik.ram@gmail.com
  3 | % Licence, CC-BY
  4 | \documentclass{beamer}
  5 | \usepackage{listings}
  6 | \usepackage{inconsolata}
  7 | \setbeamertemplate{frametitle}[default][center]
  8 | \usepackage{url}
  9 | \setcounter{secnumdepth}{-1}
 10 | \usetheme{Amsterdam}
 11 | % --------------------------------------------------------------
 12 | % Setting up some knitr options
 13 | <<setup, include=FALSE>>=
 14 | opts_chunk$set(cache=TRUE, message=FALSE)
 15 | # smaller font size for chunks
 16 | opts_chunk$set(size = 'footnotesize')
 17 | options(width = 60)
 18 | knit_hooks$set(inline = function(x) { 
 19 |   if (is.numeric(x)) return(knitr:::format_sci(x, 'latex')) 
 20 |   knitr:::hi_latex(x) 
 21 | }) 
 22 | @
 23 | 
 24 | 
 25 | % --------------------------------------------------------------
 26 | \begin{document}
 27 | \title{Data Visualization with R \& ggplot2}
 28 | \author{Karthik Ram}
 29 | \maketitle
 30 | 
 31 | % --------------------------------------------------------------
 32 | \begin{frame}[fragile]
 33 | \frametitle{Download this PDF}
 34 | \begingroup
 35 |     \fontsize{12pt}{12pt}\selectfont
 36 | \href{http://github.com/karthikram/ggplot-lecture}{github.com/karthikram/ggplot-lecture}\\
 37 | \href{https://speakerdeck.com/karthik/}{https://speakerdeck.com/karthik/}
 38 | \endgroup
 39 | \includegraphics[scale=.31]{images/git_repo.png}
 40 | \end{frame}
 41 | 
 42 | % --------------------------------------------------------------
 43 | \begin{frame}[fragile]
 44 | \frametitle{Some housekeeping}
 45 | Install some packages (make sure you also have recent copies of reshape2 and plyr)
 46 | <<installation, tidy=FALSE, echo=TRUE, eval=FALSE>>=
 47 | install.packages("ggplot2", dependencies = TRUE)
 48 | @
 49 | \end{frame}
 50 | 
 51 | 
 52 | 
 53 | % --------------------------------------------------------------
 54 | \begin{frame}[fragile]
 55 | \frametitle{Base graphics}
 56 | \begin{itemize}
 57 | \item Ugly, laborious, and verbose\\
 58 | \item There are better ways to describe statistical visualizations.\\
 59 | \end{itemize}
 60 | \end{frame}
 61 | 
 62 | \begin{frame}[fragile]
 63 | \frametitle{Why \texttt{ggplot2}?}
 64 | \begin{itemize}
 65 | \item Follows a grammar, just like any language.
 66 | \item It defines basic components that make up a sentence. In this case, the grammar defines components in a plot.
 67 | \item Grammar of graphics originally coined by Lee Wilkinson
 68 | \end{itemize}
 69 | \end{frame}
 70 | 
 71 | 
 72 | % --------------------------------------------------------------
 73 | \begin{frame}[fragile]
 74 | \frametitle{Why \texttt{ggplot2}?}
 75 | \begin{itemize}
 76 | \item  Supports a continuum of expertise.
 77 | \item Get started right away but with practice you can effortless build complex, publication quality figures.
 78 | \end{itemize}
 79 | \end{frame}
 80 | 
 81 | % --------------------------------------------------------------
 82 | \section*{Basics}
 83 | \frame{\sectionpage}
 84 | 
 85 | 
 86 | \begin{frame}[fragile]
 87 | \frametitle{Some terminology}
 88 | \begin{itemize}
 89 | \item \textbf{ggplot} - The main function where you specify the dataset and variables to plot\\
 90 | \item \textbf{geoms} - geometric objects
 91 |     \begin{itemize}
 92 |     \item geom\_point(), geom\_bar(), geom\_density(), geom\_line(), geom\_area()
 93 |     \end{itemize}
 94 | \item \textbf{aes} -  aesthetics
 95 |         \begin{itemize}
 96 |     \item shape, transparency (alpha), color, fill, linetype.
 97 |     \end{itemize}
 98 | \item \textbf{scales}  Define how your data will be plotted
 99 |         \begin{itemize}
100 |     \item \emph{continuous}, \emph{discrete}, \emph{log}
101 |     \end{itemize}
102 | \end{itemize}
103 | \end{frame}
104 | 
105 | 
106 | % --------------------------------------------------------------
107 | \section*{Assembling your first ggplot}
108 | \frame{\sectionpage}
109 | 
110 | % --------------------------------------------------------------
111 | \begin{frame}[fragile]
112 | \frametitle{The iris dataset}
113 | <<some_data, tidy=FALSE, echo=TRUE>>=
114 | head(iris)
115 | @
116 | \end{frame}
117 | 
118 | % --------------------------------------------------------------
119 | \begin{frame}[fragile]
120 | \frametitle{Let's try an example}
121 | <<first_plot , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
122 | ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width)) +
123 | geom_point()
124 | @
125 | \end{frame}
126 | 
127 | % --------------------------------------------------------------
128 | \begin{frame}[fragile]
129 | \frametitle{Basic structure}
130 | <<first_plotb , eval=FALSE, tidy=FALSE>>=
131 | ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width))
132 |  + geom_point()
133 | myplot <- ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width))
134 | myplot + geom_point()
135 |  @
136 | \begin{itemize}
137 | \item Specify the data and variables inside the \texttt{ggplot} function.
138 | \item Anything else that goes in here becomes a global setting.
139 | \item Then add layers of geometric objects, statistical models, and panels.
140 | \end{itemize}
141 | \end{frame}
142 | 
143 | % --------------------------------------------------------------
144 | \begin{frame}[fragile]
145 | \frametitle{Quick note}
146 | \begin{itemize}
147 | \item Never use \texttt{qplot} - short for quick plot.
148 | \item You'll end up unlearning and relearning a good bit.
149 | \end{itemize}
150 | 
151 | \end{frame}
152 | 
153 | 
154 | % --------------------------------------------------------------
155 | \begin{frame}[fragile]
156 | \frametitle{Increase the size of points}
157 | <<first_plot_size , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
158 | ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width)) +
159 | geom_point(size = 3)
160 | @
161 | \end{frame}
162 | 
163 | % --------------------------------------------------------------
164 | \begin{frame}[fragile]
165 | \frametitle{Add some color}
166 | <<first_plot_color , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
167 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
168 | geom_point(size = 3)
169 | @
170 | \end{frame}
171 | 
172 | % --------------------------------------------------------------
173 | \begin{frame}[fragile]
174 | \frametitle{Differentiate points by shape}
175 | <<first_plot_shape , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
176 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
177 | geom_point(aes(shape = Species), size = 3)
178 | @
179 | \end{frame}
180 | 
181 | % --------------------------------------------------------------
182 | \begin{frame}[fragile]
183 | \frametitle{Exercise 1}
184 | <<subset_data, tidy=FALSE, eval=FALSE>>=
185 | # Make a small sample of the diamonds dataset
186 | d2 <- diamonds[sample(1:dim(diamonds)[1], 1000), ]
187 | @
188 | Then generate this plot below.
189 | 
190 | <<ex1, echo = FALSE, out.width='.75\\linewidth', fig.height=3>>=
191 | d2 <- diamonds[sample(1:dim(diamonds)[1], 1000), ]
192 | ggplot(d2, aes(carat, price, color = color)) + geom_point() + theme_gray()
193 | @
194 | \end{frame}
195 | % --------------------------------------------------------------
196 | \section*{Box plots}
197 | \frame{\sectionpage}
198 | 
199 | \begin{frame}[fragile]
200 | See \texttt{?geom\_boxplot} for list of options
201 | <<boxplots1 , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
202 | library(MASS)
203 | ggplot(birthwt, aes(factor(race), bwt)) + geom_boxplot()
204 | @
205 | \end{frame}
206 | 
207 | 
208 | % --------------------------------------------------------------
209 | \section*{Histograms}
210 | \frame{\sectionpage}
211 | 
212 | % --------------------------------------------------------------
213 | \begin{frame}[fragile]
214 | See \texttt{?geom\_histogram} for list of options
215 | <<histogr , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
216 | h <- ggplot(faithful, aes(x = waiting))
217 | h + geom_histogram(binwidth = 30, colour = "black")
218 | @
219 | \end{frame}
220 | 
221 | % --------------------------------------------------------------
222 | \begin{frame}[fragile]
223 | <<histogra , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
224 | h <- ggplot(faithful, aes(x = waiting))
225 | h + geom_histogram(binwidth = 8, fill = "steelblue",
226 | colour = "black")
227 | @
228 | \end{frame}
229 | 
230 | % --------------------------------------------------------------
231 | \section*{Line plots}
232 | \frame{\sectionpage}
233 | 
234 | \begin{frame}[fragile]
235 | <<line_setup, echo=FALSE>>=
236 | setwd('~/Github/ggplot2-lecture/')
237 | @
238 | % climate <- read.csv(text = RCurl::getURL('https://raw.github.com/karthikram/ggplot-lecture/master/climate.csv'))
239 | <<linea , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
240 | climate <- read.csv("climate.csv", header = T)
241 | ggplot(climate, aes(Year, Anomaly10y)) +
242 | geom_line()
243 | @
244 | \begin{flushright}
245 | \begingroup
246 |     \fontsize{6pt}{12pt}\selectfont
247 |     \begin{verbatim}
248 |         climate <- read.csv(text =
249 |         RCurl::getURL('https://raw.github.com/karthikram/ggplot-lecture/master/climate.csv'))
250 |     \end{verbatim}
251 | \endgroup
252 | \end{flushright}
253 | \end{frame}
254 | 
255 | \begin{frame}[fragile]
256 | We can also plot confidence regions
257 | <<lineb , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
258 | ggplot(climate, aes(Year, Anomaly10y)) +
259 | geom_ribbon(aes(ymin = Anomaly10y - Unc10y,
260 | ymax = Anomaly10y + Unc10y),
261 | fill = "blue", alpha = .1) +
262 | geom_line(color = "steelblue")
263 | @
264 | \end{frame}
265 | 
266 | % --------------------------------------------------------------
267 | \begin{frame}[fragile]
268 | \frametitle{Exercise 2}
269 | \begin{itemize}
270 | \item Modify the previous plot and change it such that there are three lines instead of one with a confidence band.
271 | <<ex2, echo = FALSE, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold'>>=
272 | cplot <- ggplot(climate, aes(Year, Anomaly10y))
273 | cplot <- cplot + geom_line(size = 0.7, color = "black")
274 | cplot <- cplot + geom_line(aes(Year, Anomaly10y + Unc10y), linetype = "dashed", size = 0.7, color = "red")
275 | cplot <- cplot + geom_line(aes(Year, Anomaly10y - Unc10y), linetype = "dashed", size = 0.7, color = "red")
276 | cplot + theme_gray()
277 | @
278 | 
279 | \end{itemize}
280 | \end{frame}
281 | 
282 | 
283 | % --------------------------------------------------------------
284 | \section*{Bar plots}
285 | \frame{\sectionpage}
286 | 
287 | % --------------------------------------------------------------
288 | \begin{frame}[fragile]
289 | <<barone , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
290 | ggplot(iris, aes(Species, Sepal.Length)) +
291 | geom_bar(stat = "identity")
292 | @
293 | \end{frame}
294 | 
295 | % --------------------------------------------------------------
296 | \begin{frame}[fragile]
297 | <<bartwo , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
298 | df  <- melt(iris, id.vars = "Species")
299 | ggplot(df, aes(Species, value, fill = variable)) +
300 | geom_bar(stat = "identity")
301 | @
302 | \end{frame}
303 | 
304 | 
305 | 
306 | % --------------------------------------------------------------
307 | \section*{plyr and reshape are key for using \texttt{R}}
308 | \frame{\sectionpage}
309 | 
310 | \begin{frame}[fragile]
311 | \frametitle{plyr and reshape}
312 | These two packages are the swiss army knives of R.
313 | \begin{itemize}
314 | \item \texttt{plyr}
315 |     \begin{enumerate}
316 |     \item ddply
317 |     \item llply
318 |     \item join
319 |     \end{enumerate}
320 | \item \texttt{reshape}.
321 |     \begin{enumerate}
322 |     \item melt
323 |     \item dcast
324 |     \item acast
325 |     \end{enumerate}
326 | \end{itemize}
327 | \end{frame}
328 | 
329 | 
330 | % --------------------------------------------------------------
331 | \begin{frame}[fragile]
332 | <<bartwodata , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
333 | iris[1:2, ]
334 | df  <- melt(iris, id.vars = "Species")
335 | df[1:2, ]
336 | @
337 | \end{frame}
338 | 
339 | 
340 | % --------------------------------------------------------------
341 | \begin{frame}[fragile]
342 | <<barthree , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
343 | ggplot(df, aes(Species, value, fill = variable)) +
344 | geom_bar(stat = "identity", position = "dodge")
345 | @
346 | \end{frame}
347 | 
348 | % --------------------------------------------------------------
349 | \begin{frame}[fragile]
350 | \frametitle{Exercise 3}
351 | Using the d2 dataset you created earlier, generate this plot below. Take a quick look at the data first to see if it needs to be binned.
352 | <<ex3, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold', echo = FALSE>>=
353 | ggplot(d2, aes(clarity, fill = cut)) +
354 | geom_bar(position = "dodge",stat = "bin") + theme_gray()
355 | @
356 | \end{frame}
357 | 
358 | % --------------------------------------------------------------
359 | \begin{frame}[fragile]
360 | \frametitle{Exercise 4}
361 | \begin{itemize}
362 | \item Using the climate dataset, create a new variable called sign. Make it logical (true/false) based on the sign of Anomaly10y.
363 | \item Plot a bar plot and use \texttt{sign} variable as the fill.\\
364 | <<ex4, echo = FALSE, warning = FALSE, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold'>>=
365 | clim <- read.csv('climate.csv', header = TRUE)
366 | clim$sign <- ifelse(clim$Anomaly10y<0, FALSE, TRUE)
367 | # or as simple as
368 | # clim$sign <- clim$Anomaly10y < 0
369 | ggplot(clim, aes(Year, Anomaly10y)) + geom_bar(stat = "identity", aes(fill = sign)) + theme_gray()
370 | @
371 | 
372 | \end{itemize}
373 | \end{frame}
374 | 
375 | 
376 | % --------------------------------------------------------------
377 | \section*{Density Plots}
378 | \frame{\sectionpage}
379 | 
380 | \begin{frame}[fragile]
381 | \frametitle{Density plots}
382 | <<densityone , eval=TRUE, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
383 | ggplot(faithful, aes(waiting)) + geom_density()
384 | @
385 | \end{frame}
386 | 
387 | % --------------------------------------------------------------
388 | \begin{frame}[fragile]
389 | \frametitle{Density plots}
390 | <<densityonefove , eval=TRUE, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
391 | ggplot(faithful, aes(waiting)) +
392 | geom_density(fill = "blue", alpha = 0.1)
393 | @
394 | \end{frame}
395 | 
396 | 
397 | 
398 | % --------------------------------------------------------------
399 | \begin{frame}[fragile]
400 | <<densitytwo , , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
401 | ggplot(faithful, aes(waiting)) +
402 | geom_line(stat = "density")
403 | @
404 | \end{frame}
405 | 
406 | 
407 | % --------------------------------------------------------------
408 | \section*{Mapping Variables to colors}
409 | \frame{\sectionpage}
410 | 
411 | 
412 | % --------------------------------------------------------------
413 | \begin{frame}[fragile]
414 | \frametitle{Colors}
415 | <<color_list2, eval = FALSE, fig.width=4, fig.height=6, out.width='.75\\linewidth'>>=
416 | aes(color = variable)
417 | aes(color = "black")
418 | # Or add it as a scale
419 | scale_fill_manual(values = c("color1", "color2"))
420 | @
421 | \end{frame}
422 | 
423 | 
424 | % --------------------------------------------------------------
425 | \begin{frame}[fragile]
426 | \frametitle{The RColorBrewer package}
427 | <<color_list, eval = FALSE, fig.width=4, fig.height=5, out.width='.75\\linewidth'>>=
428 | library(RColorBrewer)
429 | display.brewer.all()
430 | @
431 | \includegraphics[scale=0.25]{images/color_palette.png}
432 | \end{frame}
433 | 
434 | % --------------------------------------------------------------
435 | \begin{frame}[fragile]
436 | \frametitle{Using a color brewer palette}
437 | <<barcolors, fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
438 | df  <- melt(iris, id.vars = "Species")
439 | ggplot(df, aes(Species, value, fill = variable)) +
440 | geom_bar(stat = "identity", position = "dodge") +
441 | scale_fill_brewer(palette = "Set1")
442 | @
443 | \end{frame}
444 | 
445 | % --------------------------------------------------------------
446 | \begin{frame}[fragile]
447 | \frametitle{Manual color scale}
448 | <<facetgridcolors, eval = TRUE, fig.width=4, fig.height=3, out.width='.75\\linewidth', tidy=FALSE>>=
449 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
450 | geom_point() +
451 | facet_grid(Species ~ .) +
452 | scale_color_manual(values = c("red", "green", "blue"))
453 | @
454 | \end{frame}
455 | 
456 | % --------------------------------------------------------------
457 | \begin{frame}[fragile]
458 | \frametitle{Refer to a color chart for beautful visualizations}
459 | \url{http://tools.medialab.sciences-po.fr/iwanthue/}
460 | \includegraphics[scale=0.25]{images/color_schemes.png}
461 | \end{frame}
462 | 
463 | % -----------------------------------
464 | 
465 | \section*{Faceting}
466 | \frame{\sectionpage}
467 | 
468 | \begin{frame}[fragile]
469 | \frametitle{Faceting along columns}
470 | <<facetgrid1, eval = TRUE, fig.width=4, fig.height=3, out.width='.75\\linewidth', tidy=FALSE>>=
471 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
472 | geom_point() +
473 | facet_grid(Species ~ .)
474 | @
475 | \end{frame}
476 | 
477 | % --------------------------------------------------------------
478 | \begin{frame}[fragile]
479 | \frametitle{and along rows}
480 | <<facet_grid2, eval = TRUE, fig.width=4, fig.height=3, out.width='.75\\linewidth', tidy= FALSE>>=
481 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
482 | geom_point() +
483 | facet_grid(. ~ Species)
484 | @
485 | \end{frame}
486 | 
487 | % --------------------------------------------------------------
488 | \begin{frame}[fragile]
489 | \frametitle{or just wrap your panels}
490 | <<facet_wrap, eval = TRUE, fig.width=4, fig.height=3, out.width='.75\\linewidth', tidy = FALSE>>=
491 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
492 | geom_point() +
493 | facet_wrap( ~ Species)
494 | @
495 | \end{frame}
496 | 
497 | % --------------------------------------------------------------
498 | \section*{Adding smoothers}
499 | \frame{\sectionpage}
500 | 
501 | 
502 | % --------------------------------------------------------------
503 | \begin{frame}[fragile]
504 | <<adding_stats,, eval = TRUE, fig.width=5, fig.height=2, out.width='.75\\linewidth', tidy=FALSE>>=
505 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
506 | geom_point(aes(shape = Species), size = 3) +
507 | geom_smooth(method = "lm")
508 | @
509 | \end{frame}
510 | 
511 | % --------------------------------------------------------------
512 | \begin{frame}[fragile]
513 | <<adding_stats2,, eval = TRUE, tidy=FALSE, fig.width=7, fig.height=3, out.width='.75\\linewidth'>>=
514 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
515 | geom_point(aes(shape = Species), size = 3) +
516 | geom_smooth(method = "lm") +
517 | facet_grid(. ~ Species)
518 | @
519 | \end{frame}
520 | 
521 | % --------------------------------------------------------------
522 | \section*{Themes}
523 | \frame{\sectionpage}
524 | 
525 | % --------------------------------------------------------------
526 | \begin{frame}[fragile]
527 | \frametitle{Adding themes}
528 | Themes are a great way to define custom plots.
529 | <<theme_list, eval = FALSE, fig.width=4, fig.height=6, out.width='.75\\linewidth'>>=
530 | + theme()
531 | # see ?theme() for more options
532 | @
533 | 
534 | \end{frame}
535 | 
536 | 
537 | % --------------------------------------------------------------
538 | \begin{frame}[fragile]
539 | \frametitle{A themed plot}
540 | <<facet_wrap_theme, eval = FALSE, fig.width=4, fig.height=6, out.width='.75\\linewidth', tidy=FALSE>>=
541 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
542 | geom_point(size = 1.2, shape = 16) +
543 | facet_wrap( ~ Species) +
544 | theme(legend.key = element_rect(fill = NA),
545 | legend.position = "bottom",
546 | strip.background = element_rect(fill = NA),
547 | axis.title.y = element_text(angle = 0))
548 | @
549 | \end{frame}
550 | 
551 | % --------------------------------------------------------------
552 | \begin{frame}[fragile]
553 | \frametitle{Adding themes}
554 | <<facet_wrap_theme_execc, eval = TRUE, echo = FALSE, fig.width=4, fig.height=3, out.width='.75\\linewidth'>>=
555 | ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
556 | geom_point(size = 1.2, shape = 16) +
557 | facet_wrap( ~ Species) +
558 | theme(legend.key = element_rect(fill = NA),
559 | legend.position = "bottom",
560 | strip.background = element_rect(fill = NA),
561 | axis.title.y = element_text(angle = 0))
562 | @
563 | \end{frame}
564 | 
565 | % --------------------------------------------------------------
566 | \begin{frame}[fragile]
567 | \frametitle{ggthemes library}
568 | <<facet_wrap_theme_exec, eval = FALSE, echo = TRUE, fig.width=4, fig.height=3, out.width='.75\\linewidth'>>=
569 | install.packages('ggthemes')
570 | library(ggthemes)
571 | # Then add one of these themes to your plot
572 |  + theme_stata()
573 |  + theme_excel()
574 |  + theme_wsj()
575 |  + theme_solarized()
576 | @
577 | \end{frame}
578 | 
579 | 
580 | % --------------------------------------------------------------
581 | \section*{Create functions to automate your plotting}
582 | \frame{\sectionpage}
583 | 
584 | % --------------------------------------------------------------
585 | \begin{frame}[fragile]
586 | \frametitle{Write functions for day to day plots}
587 | <<custom_plots, eval=FALSE, tidy=FALSE>>=
588 | my_custom_plot <- function(df, title = "", ...) {
589 |     ggplot(df, ...) +
590 |     ggtitle(title) +
591 |     whatever_geoms() +
592 |     theme(...)
593 | }
594 | @
595 | 
596 | Then just call your function to generate a plot.
597 | It's a lot easier to fix one function that do it over and over for many plots
598 | <<custom_plots2, eval=FALSE, tidy=FALSE>>=
599 | plot1 <- my_custom_plot(dataset1, title = "Figure 1")
600 | @
601 | 
602 | 
603 | \end{frame}
604 | 
605 | % --------------------------------------------------------------
606 | \section*{Scales}
607 | \frame{\sectionpage}
608 | 
609 | % --------------------------------------------------------------
610 | \begin{frame}[fragile]
611 | \frametitle{Commonly used scales}
612 | <<scale_list, eval=FALSE, tidy=FALSE>>=
613 | scale_fill_discrete(); scale_colour_discrete()
614 | scale_fill_hue(); scale_color_hue()
615 | scale_fill_manual();  scale_color_manual()
616 | scale_fill_brewer(); scale_color_brewer()
617 | scale_linetype(); scale_shape_manual()
618 | @
619 | \end{frame}
620 | 
621 | % --------------------------------------------------------------
622 | \begin{frame}[fragile]
623 | \frametitle{Adding a continuous scale}
624 | <<boxplots3 , fig.width=6, fig.height=4, out.width='.75\\linewidth', fig.show='hold',  tidy=FALSE>>=
625 | library(MASS)
626 | ggplot(birthwt, aes(factor(race), bwt)) +
627 | geom_boxplot(width = .2) +
628 | scale_y_continuous(labels = (paste0(1:4, " Kg")),
629 | breaks = seq(1000, 4000, by = 1000))
630 | @
631 | \end{frame}
632 | 
633 | 
634 | % --------------------------------------------------------------
635 | \begin{frame}[fragile]
636 | \frametitle{Another continuous scale with custom labels}
637 | <<scale_1, eval = FALSE, out.width='.75\\linewidth', tidy = FALSE>>=
638 | # Assign the plot to an object
639 | dd <- ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
640 | geom_point(size = 4, shape = 16) +
641 | facet_grid(. ~Species)
642 | # Now add a scale
643 | dd +
644 | scale_y_continuous(breaks = seq(2, 8, by = 1),
645 | labels = paste0(2:8, " cm"))
646 | @
647 | \end{frame}
648 | 
649 | 
650 | % --------------------------------------------------------------
651 | \begin{frame}[fragile]
652 | \frametitle{gradients}
653 | <<scale_2, eval = TRUE, fig.width=6, fig.height=4, out.width='.75\\linewidth', tidy = FALSE>>=
654 | h + geom_histogram( aes(fill = ..count..), color="black") +
655 | scale_fill_gradient(low="green", high="red")
656 | @
657 | \end{frame}
658 | 
659 | 
660 | 
661 | % --------------------------------------------------------------
662 | \section*{Publication quality figures}
663 | \frame{\sectionpage}
664 | 
665 | % How to save your plots
666 | % --------------------------------------------------------------
667 | \begin{frame}[fragile]
668 | \begin{itemize}
669 | \item If the plot is on your screen
670 | <<pub0, eval = FALSE, out.width='.75\\linewidth'>>=
671 | ggsave('~/path/to/figure/filename.png')
672 | @
673 | \item If your plot is assigned to an object
674 | <<pub1, eval = FALSE, out.width='.75\\linewidth'>>=
675 | ggsave(plot1, file = "~/path/to/figure/filename.png")
676 | @
677 | 
678 | \item Specify a size
679 | <<pub2, eval = FALSE, out.width='.75\\linewidth', tidy = FALSE>>=
680 | ggsave(file = "/path/to/figure/filename.png", width = 6,
681 | height =4)
682 | @
683 | \item or any format (pdf, png, eps, svg, jpg)
684 | <<pub3, eval = FALSE, out.width=".75\\linesewidth">>=
685 | ggsave(file = "/path/to/figure/filename.eps")
686 | ggsave(file = "/path/to/figure/filename.jpg")
687 | ggsave(file = "/path/to/figure/filename.pdf")
688 | @
689 | \end{itemize}
690 | \end{frame}
691 | 
692 | % --------------------------------------------------------------
693 | \begin{frame}[fragile]
694 | \frametitle{Further help}
695 | \begin{itemize}
696 | \item You've just scratched the surface with ggplot2.
697 | \item Practice
698 | \item Read the docs (either locally in \texttt{R} or at \url{http://docs.ggplot2.org/current/})
699 | \item Work together
700 | \end{itemize}
701 | \includegraphics[scale=.15]{images/chang_book.png}
702 | \includegraphics[scale=.15]{images/hadley.png}
703 | \end{frame}
704 | 
705 | % --------------------------------------------------------------
706 | % end, hope it was useful.
707 | \end{document}
708 | 


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/ggplot.pdf:
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https://raw.githubusercontent.com/karthik/ggplot-lecture/b2980ab6df3dc2053d3e7c46db44616d3db9c0c7/ggplot.pdf


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/ggplot.tex:
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   1 | % Introduction to ggplot2
   2 | % Author: Karthik Ram, karthik.ram@gmail.com
   3 | % Licence, CC-BY
   4 | \documentclass{beamer}\usepackage[]{graphicx}\usepackage[]{color}
   5 | %% maxwidth is the original width if it is less than linewidth
   6 | %% otherwise use linewidth (to make sure the graphics do not exceed the margin)
   7 | \makeatletter
   8 | \def\maxwidth{ %
   9 |   \ifdim\Gin@nat@width>\linewidth
  10 |     \linewidth
  11 |   \else
  12 |     \Gin@nat@width
  13 |   \fi
  14 | }
  15 | \makeatother
  16 | 
  17 | \definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
  18 | \newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
  19 | \newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
  20 | \newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
  21 | \newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
  22 | \newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
  23 | \newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
  24 | \newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
  25 | \newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
  26 | \newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
  27 | 
  28 | \usepackage{framed}
  29 | \makeatletter
  30 | \newenvironment{kframe}{%
  31 |  \def\at@end@of@kframe{}%
  32 |  \ifinner\ifhmode%
  33 |   \def\at@end@of@kframe{\end{minipage}}%
  34 |   \begin{minipage}{\columnwidth}%
  35 |  \fi\fi%
  36 |  \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
  37 |  \colorbox{shadecolor}{##1}\hskip-\fboxsep
  38 |      % There is no \\@totalrightmargin, so:
  39 |      \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
  40 |  \MakeFramed {\advance\hsize-\width
  41 |    \@totalleftmargin\z@ \linewidth\hsize
  42 |    \@setminipage}}%
  43 |  {\par\unskip\endMakeFramed%
  44 |  \at@end@of@kframe}
  45 | \makeatother
  46 | 
  47 | \definecolor{shadecolor}{rgb}{.97, .97, .97}
  48 | \definecolor{messagecolor}{rgb}{0, 0, 0}
  49 | \definecolor{warningcolor}{rgb}{1, 0, 1}
  50 | \definecolor{errorcolor}{rgb}{1, 0, 0}
  51 | \newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
  52 | 
  53 | \usepackage{alltt}
  54 | \usepackage{listings}
  55 | \usepackage{inconsolata}
  56 | \setbeamertemplate{frametitle}[default][center]
  57 | \usepackage{url}
  58 | \setcounter{secnumdepth}{-1}
  59 | \usetheme{Amsterdam}
  60 | % --------------------------------------------------------------
  61 | % Setting up some knitr options
  62 | 
  63 | 
  64 | 
  65 | 
  66 | % --------------------------------------------------------------
  67 | \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
  68 | \begin{document}
  69 | \title{Data Visualization with R \& ggplot2}
  70 | \author{Karthik Ram}
  71 | \maketitle
  72 | 
  73 | % --------------------------------------------------------------
  74 | \begin{frame}[fragile]
  75 | \frametitle{Download this PDF}
  76 | \begingroup
  77 |     \fontsize{12pt}{12pt}\selectfont
  78 | \href{http://github.com/karthikram/ggplot-lecture}{github.com/karthikram/ggplot-lecture}\\
  79 | \href{https://speakerdeck.com/karthik/}{https://speakerdeck.com/karthik/}
  80 | \endgroup
  81 | \includegraphics[scale=.31]{images/git_repo.png}
  82 | \end{frame}
  83 | 
  84 | % --------------------------------------------------------------
  85 | \begin{frame}[fragile]
  86 | \frametitle{Some housekeeping}
  87 | Install some packages (make sure you also have recent copies of reshape2 and plyr)
  88 | \begin{knitrout}\footnotesize
  89 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
  90 | \begin{alltt}
  91 | \hlkwd{install.packages}\hlstd{(}\hlstr{"ggplot2"}\hlstd{,} \hlkwc{dependencies} \hlstd{=} \hlnum{TRUE}\hlstd{)}
  92 | \end{alltt}
  93 | \end{kframe}
  94 | \end{knitrout}
  95 | 
  96 | \end{frame}
  97 | 
  98 | 
  99 | 
 100 | % --------------------------------------------------------------
 101 | \begin{frame}[fragile]
 102 | \frametitle{Base graphics}
 103 | \begin{itemize}
 104 | \item Ugly, laborious, and verbose\\
 105 | \item There are better ways to describe statistical visualizations.\\
 106 | \end{itemize}
 107 | \end{frame}
 108 | 
 109 | \begin{frame}[fragile]
 110 | \frametitle{Why \texttt{ggplot2}?}
 111 | \begin{itemize}
 112 | \item Follows a grammar, just like any language.
 113 | \item It defines basic components that make up a sentence. In this case, the grammar defines components in a plot.
 114 | \item Grammar of graphics originally coined by Lee Wilkinson
 115 | \end{itemize}
 116 | \end{frame}
 117 | 
 118 | 
 119 | % --------------------------------------------------------------
 120 | \begin{frame}[fragile]
 121 | \frametitle{Why \texttt{ggplot2}?}
 122 | \begin{itemize}
 123 | \item  Supports a continuum of expertise.
 124 | \item Get started right away but with practice you can effortless build complex, publication quality figures.
 125 | \end{itemize}
 126 | \end{frame}
 127 | 
 128 | % --------------------------------------------------------------
 129 | \section*{Basics}
 130 | \frame{\sectionpage}
 131 | 
 132 | 
 133 | \begin{frame}[fragile]
 134 | \frametitle{Some terminology}
 135 | \begin{itemize}
 136 | \item \textbf{ggplot} - The main function where you specify the dataset and variables to plot\\
 137 | \item \textbf{geoms} - geometric objects
 138 |     \begin{itemize}
 139 |     \item geom\_point(), geom\_bar(), geom\_density(), geom\_line(), geom\_area()
 140 |     \end{itemize}
 141 | \item \textbf{aes} -  aesthetics
 142 |         \begin{itemize}
 143 |     \item shape, transparency (alpha), color, fill, linetype.
 144 |     \end{itemize}
 145 | \item \textbf{scales}  Define how your data will be plotted
 146 |         \begin{itemize}
 147 |     \item \emph{continuous}, \emph{discrete}, \emph{log}
 148 |     \end{itemize}
 149 | \end{itemize}
 150 | \end{frame}
 151 | 
 152 | 
 153 | % --------------------------------------------------------------
 154 | \section*{Assembling your first ggplot}
 155 | \frame{\sectionpage}
 156 | 
 157 | % --------------------------------------------------------------
 158 | \begin{frame}[fragile]
 159 | \frametitle{The iris dataset}
 160 | \begin{knitrout}\footnotesize
 161 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 162 | \begin{alltt}
 163 | \hlkwd{head}\hlstd{(iris)}
 164 | \end{alltt}
 165 | \begin{verbatim}
 166 | ##   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
 167 | ## 1          5.1         3.5          1.4         0.2  setosa
 168 | ## 2          4.9         3.0          1.4         0.2  setosa
 169 | ## 3          4.7         3.2          1.3         0.2  setosa
 170 | ## 4          4.6         3.1          1.5         0.2  setosa
 171 | ## 5          5.0         3.6          1.4         0.2  setosa
 172 | ## 6          5.4         3.9          1.7         0.4  setosa
 173 | \end{verbatim}
 174 | \end{kframe}
 175 | \end{knitrout}
 176 | 
 177 | \end{frame}
 178 | 
 179 | % --------------------------------------------------------------
 180 | \begin{frame}[fragile]
 181 | \frametitle{Let's try an example}
 182 | \begin{knitrout}\footnotesize
 183 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 184 | \begin{alltt}
 185 | \hlkwd{ggplot}\hlstd{(}\hlkwc{data} \hlstd{= iris,} \hlkwd{aes}\hlstd{(}\hlkwc{x} \hlstd{= Sepal.Length,} \hlkwc{y} \hlstd{= Sepal.Width))} \hlopt{+}
 186 | \hlkwd{geom_point}\hlstd{()}
 187 | \end{alltt}
 188 | \end{kframe}
 189 | \includegraphics[width=.75\linewidth]{figure/first_plot_} 
 190 | 
 191 | \end{knitrout}
 192 | 
 193 | \end{frame}
 194 | 
 195 | % --------------------------------------------------------------
 196 | \begin{frame}[fragile]
 197 | \frametitle{Basic structure}
 198 | \begin{knitrout}\footnotesize
 199 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 200 | \begin{alltt}
 201 | \hlkwd{ggplot}\hlstd{(}\hlkwc{data} \hlstd{= iris,} \hlkwd{aes}\hlstd{(}\hlkwc{x} \hlstd{= Sepal.Length,} \hlkwc{y} \hlstd{= Sepal.Width))}
 202 |  \hlopt{+} \hlkwd{geom_point}\hlstd{()}
 203 | \hlstd{myplot} \hlkwb{<-} \hlkwd{ggplot}\hlstd{(}\hlkwc{data} \hlstd{= iris,} \hlkwd{aes}\hlstd{(}\hlkwc{x} \hlstd{= Sepal.Length,} \hlkwc{y} \hlstd{= Sepal.Width))}
 204 | \hlstd{myplot} \hlopt{+} \hlkwd{geom_point}\hlstd{()}
 205 | \end{alltt}
 206 | \end{kframe}
 207 | \end{knitrout}
 208 | 
 209 | \begin{itemize}
 210 | \item Specify the data and variables inside the \texttt{ggplot} function.
 211 | \item Anything else that goes in here becomes a global setting.
 212 | \item Then add layers of geometric objects, statistical models, and panels.
 213 | \end{itemize}
 214 | \end{frame}
 215 | 
 216 | % --------------------------------------------------------------
 217 | \begin{frame}[fragile]
 218 | \frametitle{Quick note}
 219 | \begin{itemize}
 220 | \item Never use \texttt{qplot} - short for quick plot.
 221 | \item You'll end up unlearning and relearning a good bit.
 222 | \end{itemize}
 223 | 
 224 | \end{frame}
 225 | 
 226 | 
 227 | % --------------------------------------------------------------
 228 | \begin{frame}[fragile]
 229 | \frametitle{Increase the size of points}
 230 | \begin{knitrout}\footnotesize
 231 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 232 | \begin{alltt}
 233 | \hlkwd{ggplot}\hlstd{(}\hlkwc{data} \hlstd{= iris,} \hlkwd{aes}\hlstd{(}\hlkwc{x} \hlstd{= Sepal.Length,} \hlkwc{y} \hlstd{= Sepal.Width))} \hlopt{+}
 234 | \hlkwd{geom_point}\hlstd{(}\hlkwc{size} \hlstd{=} \hlnum{3}\hlstd{)}
 235 | \end{alltt}
 236 | \end{kframe}
 237 | \includegraphics[width=.75\linewidth]{figure/first_plot_size_} 
 238 | 
 239 | \end{knitrout}
 240 | 
 241 | \end{frame}
 242 | 
 243 | % --------------------------------------------------------------
 244 | \begin{frame}[fragile]
 245 | \frametitle{Add some color}
 246 | \begin{knitrout}\footnotesize
 247 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 248 | \begin{alltt}
 249 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 250 | \hlkwd{geom_point}\hlstd{(}\hlkwc{size} \hlstd{=} \hlnum{3}\hlstd{)}
 251 | \end{alltt}
 252 | \end{kframe}
 253 | \includegraphics[width=.75\linewidth]{figure/first_plot_color_} 
 254 | 
 255 | \end{knitrout}
 256 | 
 257 | \end{frame}
 258 | 
 259 | % --------------------------------------------------------------
 260 | \begin{frame}[fragile]
 261 | \frametitle{Differentiate points by shape}
 262 | \begin{knitrout}\footnotesize
 263 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 264 | \begin{alltt}
 265 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 266 | \hlkwd{geom_point}\hlstd{(}\hlkwd{aes}\hlstd{(}\hlkwc{shape} \hlstd{= Species),} \hlkwc{size} \hlstd{=} \hlnum{3}\hlstd{)}
 267 | \end{alltt}
 268 | \end{kframe}
 269 | \includegraphics[width=.75\linewidth]{figure/first_plot_shape_} 
 270 | 
 271 | \end{knitrout}
 272 | 
 273 | \end{frame}
 274 | 
 275 | % --------------------------------------------------------------
 276 | \begin{frame}[fragile]
 277 | \frametitle{Exercise 1}
 278 | \begin{knitrout}\footnotesize
 279 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 280 | \begin{alltt}
 281 | \hlcom{# Make a small sample of the diamonds dataset}
 282 | \hlstd{d2} \hlkwb{<-} \hlstd{diamonds[}\hlkwd{sample}\hlstd{(}\hlnum{1}\hlopt{:}\hlkwd{dim}\hlstd{(diamonds)[}\hlnum{1}\hlstd{],} \hlnum{1000}\hlstd{), ]}
 283 | \end{alltt}
 284 | \end{kframe}
 285 | \end{knitrout}
 286 | 
 287 | Then generate this plot below.
 288 | 
 289 | \begin{knitrout}\footnotesize
 290 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}
 291 | \includegraphics[width=.75\linewidth]{figure/ex1} 
 292 | 
 293 | \end{knitrout}
 294 | 
 295 | \end{frame}
 296 | % --------------------------------------------------------------
 297 | \section*{Box plots}
 298 | \frame{\sectionpage}
 299 | 
 300 | \begin{frame}[fragile]
 301 | See \texttt{?geom\_boxplot} for list of options
 302 | \begin{knitrout}\footnotesize
 303 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 304 | \begin{alltt}
 305 | \hlkwd{library}\hlstd{(MASS)}
 306 | \hlkwd{ggplot}\hlstd{(birthwt,} \hlkwd{aes}\hlstd{(}\hlkwd{factor}\hlstd{(race), bwt))} \hlopt{+} \hlkwd{geom_boxplot}\hlstd{()}
 307 | \end{alltt}
 308 | \end{kframe}
 309 | \includegraphics[width=.75\linewidth]{figure/boxplots1_} 
 310 | 
 311 | \end{knitrout}
 312 | 
 313 | \end{frame}
 314 | 
 315 | 
 316 | % --------------------------------------------------------------
 317 | \section*{Histograms}
 318 | \frame{\sectionpage}
 319 | 
 320 | % --------------------------------------------------------------
 321 | \begin{frame}[fragile]
 322 | See \texttt{?geom\_histogram} for list of options
 323 | \begin{knitrout}\footnotesize
 324 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 325 | \begin{alltt}
 326 | \hlstd{h} \hlkwb{<-} \hlkwd{ggplot}\hlstd{(faithful,} \hlkwd{aes}\hlstd{(}\hlkwc{x} \hlstd{= waiting))}
 327 | \hlstd{h} \hlopt{+} \hlkwd{geom_histogram}\hlstd{(}\hlkwc{binwidth} \hlstd{=} \hlnum{30}\hlstd{,} \hlkwc{colour} \hlstd{=} \hlstr{"black"}\hlstd{)}
 328 | \end{alltt}
 329 | \end{kframe}
 330 | \includegraphics[width=.75\linewidth]{figure/histogr_} 
 331 | 
 332 | \end{knitrout}
 333 | 
 334 | \end{frame}
 335 | 
 336 | % --------------------------------------------------------------
 337 | \begin{frame}[fragile]
 338 | \begin{knitrout}\footnotesize
 339 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 340 | \begin{alltt}
 341 | \hlstd{h} \hlkwb{<-} \hlkwd{ggplot}\hlstd{(faithful,} \hlkwd{aes}\hlstd{(}\hlkwc{x} \hlstd{= waiting))}
 342 | \hlstd{h} \hlopt{+} \hlkwd{geom_histogram}\hlstd{(}\hlkwc{binwidth} \hlstd{=} \hlnum{8}\hlstd{,} \hlkwc{fill} \hlstd{=} \hlstr{"steelblue"}\hlstd{,}
 343 | \hlkwc{colour} \hlstd{=} \hlstr{"black"}\hlstd{)}
 344 | \end{alltt}
 345 | \end{kframe}
 346 | \includegraphics[width=.75\linewidth]{figure/histogra_} 
 347 | 
 348 | \end{knitrout}
 349 | 
 350 | \end{frame}
 351 | 
 352 | % --------------------------------------------------------------
 353 | \section*{Line plots}
 354 | \frame{\sectionpage}
 355 | 
 356 | \begin{frame}[fragile]
 357 | 
 358 | 
 359 | % climate <- read.csv(text = RCurl::getURL('https://raw.github.com/karthikram/ggplot-lecture/master/climate.csv'))
 360 | \begin{knitrout}\footnotesize
 361 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 362 | \begin{alltt}
 363 | \hlstd{climate} \hlkwb{<-} \hlkwd{read.csv}\hlstd{(}\hlstr{"climate.csv"}\hlstd{,} \hlkwc{header} \hlstd{= T)}
 364 | \hlkwd{ggplot}\hlstd{(climate,} \hlkwd{aes}\hlstd{(Year, Anomaly10y))} \hlopt{+}
 365 | \hlkwd{geom_line}\hlstd{()}
 366 | \end{alltt}
 367 | \end{kframe}
 368 | \includegraphics[width=.75\linewidth]{figure/linea_} 
 369 | 
 370 | \end{knitrout}
 371 | 
 372 | \begin{flushright}
 373 | \begingroup
 374 |     \fontsize{6pt}{12pt}\selectfont
 375 |     \begin{verbatim}
 376 |         climate <- read.csv(text =
 377 |         RCurl::getURL('https://raw.github.com/karthikram/ggplot-lecture/master/climate.csv'))
 378 |     \end{verbatim}
 379 | \endgroup
 380 | \end{flushright}
 381 | \end{frame}
 382 | 
 383 | \begin{frame}[fragile]
 384 | We can also plot confidence regions
 385 | \begin{knitrout}\footnotesize
 386 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 387 | \begin{alltt}
 388 | \hlkwd{ggplot}\hlstd{(climate,} \hlkwd{aes}\hlstd{(Year, Anomaly10y))} \hlopt{+}
 389 | \hlkwd{geom_ribbon}\hlstd{(}\hlkwd{aes}\hlstd{(}\hlkwc{ymin} \hlstd{= Anomaly10y} \hlopt{-} \hlstd{Unc10y,}
 390 | \hlkwc{ymax} \hlstd{= Anomaly10y} \hlopt{+} \hlstd{Unc10y),}
 391 | \hlkwc{fill} \hlstd{=} \hlstr{"blue"}\hlstd{,} \hlkwc{alpha} \hlstd{=} \hlnum{.1}\hlstd{)} \hlopt{+}
 392 | \hlkwd{geom_line}\hlstd{(}\hlkwc{color} \hlstd{=} \hlstr{"steelblue"}\hlstd{)}
 393 | \end{alltt}
 394 | \end{kframe}
 395 | \includegraphics[width=.75\linewidth]{figure/lineb_} 
 396 | 
 397 | \end{knitrout}
 398 | 
 399 | \end{frame}
 400 | 
 401 | % --------------------------------------------------------------
 402 | \begin{frame}[fragile]
 403 | \frametitle{Exercise 2}
 404 | \begin{itemize}
 405 | \item Modify the previous plot and change it such that there are three lines instead of one with a confidence band.
 406 | \begin{knitrout}\footnotesize
 407 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}
 408 | \includegraphics[width=.75\linewidth]{figure/ex2} 
 409 | 
 410 | \end{knitrout}
 411 | 
 412 | 
 413 | \end{itemize}
 414 | \end{frame}
 415 | 
 416 | 
 417 | % --------------------------------------------------------------
 418 | \section*{Bar plots}
 419 | \frame{\sectionpage}
 420 | 
 421 | % --------------------------------------------------------------
 422 | \begin{frame}[fragile]
 423 | \begin{knitrout}\footnotesize
 424 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 425 | \begin{alltt}
 426 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Species, Sepal.Length))} \hlopt{+}
 427 | \hlkwd{geom_bar}\hlstd{(}\hlkwc{stat} \hlstd{=} \hlstr{"identity"}\hlstd{)}
 428 | \end{alltt}
 429 | \end{kframe}
 430 | \includegraphics[width=.75\linewidth]{figure/barone_} 
 431 | 
 432 | \end{knitrout}
 433 | 
 434 | \end{frame}
 435 | 
 436 | % --------------------------------------------------------------
 437 | \begin{frame}[fragile]
 438 | \begin{knitrout}\footnotesize
 439 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 440 | \begin{alltt}
 441 | \hlstd{df}  \hlkwb{<-} \hlkwd{melt}\hlstd{(iris,} \hlkwc{id.vars} \hlstd{=} \hlstr{"Species"}\hlstd{)}
 442 | \hlkwd{ggplot}\hlstd{(df,} \hlkwd{aes}\hlstd{(Species, value,} \hlkwc{fill} \hlstd{= variable))} \hlopt{+}
 443 | \hlkwd{geom_bar}\hlstd{(}\hlkwc{stat} \hlstd{=} \hlstr{"identity"}\hlstd{)}
 444 | \end{alltt}
 445 | \end{kframe}
 446 | \includegraphics[width=.75\linewidth]{figure/bartwo_} 
 447 | 
 448 | \end{knitrout}
 449 | 
 450 | \end{frame}
 451 | 
 452 | 
 453 | 
 454 | % --------------------------------------------------------------
 455 | \section*{plyr and reshape are key for using \texttt{R}}
 456 | \frame{\sectionpage}
 457 | 
 458 | \begin{frame}[fragile]
 459 | \frametitle{plyr and reshape}
 460 | These two packages are the swiss army knives of R.
 461 | \begin{itemize}
 462 | \item \texttt{plyr}
 463 |     \begin{enumerate}
 464 |     \item ddply
 465 |     \item llply
 466 |     \item join
 467 |     \end{enumerate}
 468 | \item \texttt{reshape}.
 469 |     \begin{enumerate}
 470 |     \item melt
 471 |     \item dcast
 472 |     \item acast
 473 |     \end{enumerate}
 474 | \end{itemize}
 475 | \end{frame}
 476 | 
 477 | 
 478 | % --------------------------------------------------------------
 479 | \begin{frame}[fragile]
 480 | \begin{knitrout}\footnotesize
 481 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 482 | \begin{alltt}
 483 | \hlstd{iris[}\hlnum{1}\hlopt{:}\hlnum{2}\hlstd{, ]}
 484 | \end{alltt}
 485 | \begin{verbatim}
 486 | ##   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
 487 | ## 1          5.1         3.5          1.4         0.2  setosa
 488 | ## 2          4.9         3.0          1.4         0.2  setosa
 489 | \end{verbatim}
 490 | \begin{alltt}
 491 | \hlstd{df}  \hlkwb{<-} \hlkwd{melt}\hlstd{(iris,} \hlkwc{id.vars} \hlstd{=} \hlstr{"Species"}\hlstd{)}
 492 | \hlstd{df[}\hlnum{1}\hlopt{:}\hlnum{2}\hlstd{, ]}
 493 | \end{alltt}
 494 | \begin{verbatim}
 495 | ##   Species     variable value
 496 | ## 1  setosa Sepal.Length   5.1
 497 | ## 2  setosa Sepal.Length   4.9
 498 | \end{verbatim}
 499 | \end{kframe}
 500 | \end{knitrout}
 501 | 
 502 | \end{frame}
 503 | 
 504 | 
 505 | % --------------------------------------------------------------
 506 | \begin{frame}[fragile]
 507 | \begin{knitrout}\footnotesize
 508 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 509 | \begin{alltt}
 510 | \hlkwd{ggplot}\hlstd{(df,} \hlkwd{aes}\hlstd{(Species, value,} \hlkwc{fill} \hlstd{= variable))} \hlopt{+}
 511 | \hlkwd{geom_bar}\hlstd{(}\hlkwc{stat} \hlstd{=} \hlstr{"identity"}\hlstd{,} \hlkwc{position} \hlstd{=} \hlstr{"dodge"}\hlstd{)}
 512 | \end{alltt}
 513 | \end{kframe}
 514 | \includegraphics[width=.75\linewidth]{figure/barthree_} 
 515 | 
 516 | \end{knitrout}
 517 | 
 518 | \end{frame}
 519 | 
 520 | % --------------------------------------------------------------
 521 | \begin{frame}[fragile]
 522 | \frametitle{Exercise 3}
 523 | Using the d2 dataset you created earlier, generate this plot below. Take a quick look at the data first to see if it needs to be binned.
 524 | \begin{knitrout}\footnotesize
 525 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}
 526 | \includegraphics[width=.75\linewidth]{figure/ex3} 
 527 | 
 528 | \end{knitrout}
 529 | 
 530 | \end{frame}
 531 | 
 532 | % --------------------------------------------------------------
 533 | \begin{frame}[fragile]
 534 | \frametitle{Exercise 4}
 535 | \begin{itemize}
 536 | \item Using the climate dataset, create a new variable called sign. Make it logical (true/false) based on the sign of Anomaly10y.
 537 | \item Plot a bar plot and use \texttt{sign} variable as the fill.\\
 538 | \begin{knitrout}\footnotesize
 539 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}
 540 | \includegraphics[width=.75\linewidth]{figure/ex4} 
 541 | 
 542 | \end{knitrout}
 543 | 
 544 | 
 545 | \end{itemize}
 546 | \end{frame}
 547 | 
 548 | 
 549 | % --------------------------------------------------------------
 550 | \section*{Density Plots}
 551 | \frame{\sectionpage}
 552 | 
 553 | \begin{frame}[fragile]
 554 | \frametitle{Density plots}
 555 | \begin{knitrout}\footnotesize
 556 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 557 | \begin{alltt}
 558 | \hlkwd{ggplot}\hlstd{(faithful,} \hlkwd{aes}\hlstd{(waiting))} \hlopt{+} \hlkwd{geom_density}\hlstd{()}
 559 | \end{alltt}
 560 | \end{kframe}
 561 | \includegraphics[width=.75\linewidth]{figure/densityone_} 
 562 | 
 563 | \end{knitrout}
 564 | 
 565 | \end{frame}
 566 | 
 567 | % --------------------------------------------------------------
 568 | \begin{frame}[fragile]
 569 | \frametitle{Density plots}
 570 | \begin{knitrout}\footnotesize
 571 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 572 | \begin{alltt}
 573 | \hlkwd{ggplot}\hlstd{(faithful,} \hlkwd{aes}\hlstd{(waiting))} \hlopt{+}
 574 | \hlkwd{geom_density}\hlstd{(}\hlkwc{fill} \hlstd{=} \hlstr{"blue"}\hlstd{,} \hlkwc{alpha} \hlstd{=} \hlnum{0.1}\hlstd{)}
 575 | \end{alltt}
 576 | \end{kframe}
 577 | \includegraphics[width=.75\linewidth]{figure/densityonefove_} 
 578 | 
 579 | \end{knitrout}
 580 | 
 581 | \end{frame}
 582 | 
 583 | 
 584 | 
 585 | % --------------------------------------------------------------
 586 | \begin{frame}[fragile]
 587 | \begin{knitrout}\footnotesize
 588 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 589 | \begin{alltt}
 590 | \hlkwd{ggplot}\hlstd{(faithful,} \hlkwd{aes}\hlstd{(waiting))} \hlopt{+}
 591 | \hlkwd{geom_line}\hlstd{(}\hlkwc{stat} \hlstd{=} \hlstr{"density"}\hlstd{)}
 592 | \end{alltt}
 593 | \end{kframe}
 594 | \includegraphics[width=.75\linewidth]{figure/densitytwo___} 
 595 | 
 596 | \end{knitrout}
 597 | 
 598 | \end{frame}
 599 | 
 600 | 
 601 | % --------------------------------------------------------------
 602 | \section*{Mapping Variables to colors}
 603 | \frame{\sectionpage}
 604 | 
 605 | 
 606 | % --------------------------------------------------------------
 607 | \begin{frame}[fragile]
 608 | \frametitle{Colors}
 609 | \begin{knitrout}\footnotesize
 610 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 611 | \begin{alltt}
 612 | \hlkwd{aes}\hlstd{(}\hlkwc{color} \hlstd{= variable)}
 613 | \hlkwd{aes}\hlstd{(}\hlkwc{color} \hlstd{=} \hlstr{"black"}\hlstd{)}
 614 | \hlcom{# Or add it as a scale}
 615 | \hlkwd{scale_fill_manual}\hlstd{(}\hlkwc{values} \hlstd{=} \hlkwd{c}\hlstd{(}\hlstr{"color1"}\hlstd{,} \hlstr{"color2"}\hlstd{))}
 616 | \end{alltt}
 617 | \end{kframe}
 618 | \end{knitrout}
 619 | 
 620 | \end{frame}
 621 | 
 622 | 
 623 | % --------------------------------------------------------------
 624 | \begin{frame}[fragile]
 625 | \frametitle{The RColorBrewer package}
 626 | \begin{knitrout}\footnotesize
 627 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 628 | \begin{alltt}
 629 | \hlkwd{library}\hlstd{(RColorBrewer)}
 630 | \hlkwd{display.brewer.all}\hlstd{()}
 631 | \end{alltt}
 632 | \end{kframe}
 633 | \end{knitrout}
 634 | 
 635 | \includegraphics[scale=0.25]{images/color_palette.png}
 636 | \end{frame}
 637 | 
 638 | % --------------------------------------------------------------
 639 | \begin{frame}[fragile]
 640 | \frametitle{Using a color brewer palette}
 641 | \begin{knitrout}\footnotesize
 642 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 643 | \begin{alltt}
 644 | \hlstd{df}  \hlkwb{<-} \hlkwd{melt}\hlstd{(iris,} \hlkwc{id.vars} \hlstd{=} \hlstr{"Species"}\hlstd{)}
 645 | \hlkwd{ggplot}\hlstd{(df,} \hlkwd{aes}\hlstd{(Species, value,} \hlkwc{fill} \hlstd{= variable))} \hlopt{+}
 646 | \hlkwd{geom_bar}\hlstd{(}\hlkwc{stat} \hlstd{=} \hlstr{"identity"}\hlstd{,} \hlkwc{position} \hlstd{=} \hlstr{"dodge"}\hlstd{)} \hlopt{+}
 647 | \hlkwd{scale_fill_brewer}\hlstd{(}\hlkwc{palette} \hlstd{=} \hlstr{"Set1"}\hlstd{)}
 648 | \end{alltt}
 649 | \end{kframe}
 650 | \includegraphics[width=.75\linewidth]{figure/barcolors} 
 651 | 
 652 | \end{knitrout}
 653 | 
 654 | \end{frame}
 655 | 
 656 | % --------------------------------------------------------------
 657 | \begin{frame}[fragile]
 658 | \frametitle{Manual color scale}
 659 | \begin{knitrout}\footnotesize
 660 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 661 | \begin{alltt}
 662 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 663 | \hlkwd{geom_point}\hlstd{()} \hlopt{+}
 664 | \hlkwd{facet_grid}\hlstd{(Species} \hlopt{~} \hlstd{.)} \hlopt{+}
 665 | \hlkwd{scale_color_manual}\hlstd{(}\hlkwc{values} \hlstd{=} \hlkwd{c}\hlstd{(}\hlstr{"red"}\hlstd{,} \hlstr{"green"}\hlstd{,} \hlstr{"blue"}\hlstd{))}
 666 | \end{alltt}
 667 | \end{kframe}
 668 | \includegraphics[width=.75\linewidth]{figure/facetgridcolors} 
 669 | 
 670 | \end{knitrout}
 671 | 
 672 | \end{frame}
 673 | 
 674 | % --------------------------------------------------------------
 675 | \begin{frame}[fragile]
 676 | \frametitle{Refer to a color chart for beautful visualizations}
 677 | \url{http://tools.medialab.sciences-po.fr/iwanthue/}
 678 | \includegraphics[scale=0.25]{images/color_schemes.png}
 679 | \end{frame}
 680 | 
 681 | % -----------------------------------
 682 | 
 683 | \section*{Faceting}
 684 | \frame{\sectionpage}
 685 | 
 686 | \begin{frame}[fragile]
 687 | \frametitle{Faceting along columns}
 688 | \begin{knitrout}\footnotesize
 689 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 690 | \begin{alltt}
 691 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 692 | \hlkwd{geom_point}\hlstd{()} \hlopt{+}
 693 | \hlkwd{facet_grid}\hlstd{(Species} \hlopt{~} \hlstd{.)}
 694 | \end{alltt}
 695 | \end{kframe}
 696 | \includegraphics[width=.75\linewidth]{figure/facetgrid1} 
 697 | 
 698 | \end{knitrout}
 699 | 
 700 | \end{frame}
 701 | 
 702 | % --------------------------------------------------------------
 703 | \begin{frame}[fragile]
 704 | \frametitle{and along rows}
 705 | \begin{knitrout}\footnotesize
 706 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 707 | \begin{alltt}
 708 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 709 | \hlkwd{geom_point}\hlstd{()} \hlopt{+}
 710 | \hlkwd{facet_grid}\hlstd{(.} \hlopt{~} \hlstd{Species)}
 711 | \end{alltt}
 712 | \end{kframe}
 713 | \includegraphics[width=.75\linewidth]{figure/facet_grid2} 
 714 | 
 715 | \end{knitrout}
 716 | 
 717 | \end{frame}
 718 | 
 719 | % --------------------------------------------------------------
 720 | \begin{frame}[fragile]
 721 | \frametitle{or just wrap your panels}
 722 | \begin{knitrout}\footnotesize
 723 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 724 | \begin{alltt}
 725 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 726 | \hlkwd{geom_point}\hlstd{()} \hlopt{+}
 727 | \hlkwd{facet_wrap}\hlstd{(} \hlopt{~} \hlstd{Species)}
 728 | \end{alltt}
 729 | \end{kframe}
 730 | \includegraphics[width=.75\linewidth]{figure/facet_wrap} 
 731 | 
 732 | \end{knitrout}
 733 | 
 734 | \end{frame}
 735 | 
 736 | % --------------------------------------------------------------
 737 | \section*{Adding smoothers}
 738 | \frame{\sectionpage}
 739 | 
 740 | 
 741 | % --------------------------------------------------------------
 742 | \begin{frame}[fragile]
 743 | \begin{knitrout}\footnotesize
 744 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 745 | \begin{alltt}
 746 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 747 | \hlkwd{geom_point}\hlstd{(}\hlkwd{aes}\hlstd{(}\hlkwc{shape} \hlstd{= Species),} \hlkwc{size} \hlstd{=} \hlnum{3}\hlstd{)} \hlopt{+}
 748 | \hlkwd{geom_smooth}\hlstd{(}\hlkwc{method} \hlstd{=} \hlstr{"lm"}\hlstd{)}
 749 | \end{alltt}
 750 | \end{kframe}
 751 | \includegraphics[width=.75\linewidth]{figure/adding_stats_} 
 752 | 
 753 | \end{knitrout}
 754 | 
 755 | \end{frame}
 756 | 
 757 | % --------------------------------------------------------------
 758 | \begin{frame}[fragile]
 759 | \begin{knitrout}\footnotesize
 760 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 761 | \begin{alltt}
 762 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 763 | \hlkwd{geom_point}\hlstd{(}\hlkwd{aes}\hlstd{(}\hlkwc{shape} \hlstd{= Species),} \hlkwc{size} \hlstd{=} \hlnum{3}\hlstd{)} \hlopt{+}
 764 | \hlkwd{geom_smooth}\hlstd{(}\hlkwc{method} \hlstd{=} \hlstr{"lm"}\hlstd{)} \hlopt{+}
 765 | \hlkwd{facet_grid}\hlstd{(.} \hlopt{~} \hlstd{Species)}
 766 | \end{alltt}
 767 | \end{kframe}
 768 | \includegraphics[width=.75\linewidth]{figure/adding_stats2_} 
 769 | 
 770 | \end{knitrout}
 771 | 
 772 | \end{frame}
 773 | 
 774 | % --------------------------------------------------------------
 775 | \section*{Themes}
 776 | \frame{\sectionpage}
 777 | 
 778 | % --------------------------------------------------------------
 779 | \begin{frame}[fragile]
 780 | \frametitle{Adding themes}
 781 | Themes are a great way to define custom plots.
 782 | \begin{knitrout}\footnotesize
 783 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 784 | \begin{alltt}
 785 | \hlopt{+}\hlkwd{theme}\hlstd{()}
 786 | \hlcom{# see ?theme() for more options}
 787 | \end{alltt}
 788 | \end{kframe}
 789 | \end{knitrout}
 790 | 
 791 | 
 792 | \end{frame}
 793 | 
 794 | 
 795 | % --------------------------------------------------------------
 796 | \begin{frame}[fragile]
 797 | \frametitle{A themed plot}
 798 | \begin{knitrout}\footnotesize
 799 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 800 | \begin{alltt}
 801 | \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 802 | \hlkwd{geom_point}\hlstd{(}\hlkwc{size} \hlstd{=} \hlnum{1.2}\hlstd{,} \hlkwc{shape} \hlstd{=} \hlnum{16}\hlstd{)} \hlopt{+}
 803 | \hlkwd{facet_wrap}\hlstd{(} \hlopt{~} \hlstd{Species)} \hlopt{+}
 804 | \hlkwd{theme}\hlstd{(}\hlkwc{legend.key} \hlstd{=} \hlkwd{element_rect}\hlstd{(}\hlkwc{fill} \hlstd{=} \hlnum{NA}\hlstd{),}
 805 | \hlkwc{legend.position} \hlstd{=} \hlstr{"bottom"}\hlstd{,}
 806 | \hlkwc{strip.background} \hlstd{=} \hlkwd{element_rect}\hlstd{(}\hlkwc{fill} \hlstd{=} \hlnum{NA}\hlstd{),}
 807 | \hlkwc{axis.title.y} \hlstd{=} \hlkwd{element_text}\hlstd{(}\hlkwc{angle} \hlstd{=} \hlnum{0}\hlstd{))}
 808 | \end{alltt}
 809 | \end{kframe}
 810 | \end{knitrout}
 811 | 
 812 | \end{frame}
 813 | 
 814 | % --------------------------------------------------------------
 815 | \begin{frame}[fragile]
 816 | \frametitle{Adding themes}
 817 | \begin{knitrout}\footnotesize
 818 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}
 819 | \includegraphics[width=.75\linewidth]{figure/facet_wrap_theme_execc} 
 820 | 
 821 | \end{knitrout}
 822 | 
 823 | \end{frame}
 824 | 
 825 | % --------------------------------------------------------------
 826 | \begin{frame}[fragile]
 827 | \frametitle{ggthemes library}
 828 | \begin{knitrout}\footnotesize
 829 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 830 | \begin{alltt}
 831 | \hlkwd{install.packages}\hlstd{(}\hlstr{"ggthemes"}\hlstd{)}
 832 | \hlkwd{library}\hlstd{(ggthemes)}
 833 | \hlcom{# Then add one of these themes to your plot}
 834 | \hlopt{+}\hlkwd{theme_stata}\hlstd{()}
 835 | \hlopt{+}\hlkwd{theme_excel}\hlstd{()}
 836 | \hlopt{+}\hlkwd{theme_wsj}\hlstd{()}
 837 | \hlopt{+}\hlkwd{theme_solarized}\hlstd{()}
 838 | \end{alltt}
 839 | \end{kframe}
 840 | \end{knitrout}
 841 | 
 842 | \end{frame}
 843 | 
 844 | 
 845 | % --------------------------------------------------------------
 846 | \section*{Create functions to automate your plotting}
 847 | \frame{\sectionpage}
 848 | 
 849 | % --------------------------------------------------------------
 850 | \begin{frame}[fragile]
 851 | \frametitle{Write functions for day to day plots}
 852 | \begin{knitrout}\footnotesize
 853 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 854 | \begin{alltt}
 855 | \hlstd{my_custom_plot} \hlkwb{<-} \hlkwa{function}\hlstd{(}\hlkwc{df}\hlstd{,} \hlkwc{title} \hlstd{=} \hlstr{""}\hlstd{,} \hlkwc{...}\hlstd{) \{}
 856 |     \hlkwd{ggplot}\hlstd{(df, ...)} \hlopt{+}
 857 |     \hlkwd{ggtitle}\hlstd{(title)} \hlopt{+}
 858 |     \hlkwd{whatever_geoms}\hlstd{()} \hlopt{+}
 859 |     \hlkwd{theme}\hlstd{(...)}
 860 | \hlstd{\}}
 861 | \end{alltt}
 862 | \end{kframe}
 863 | \end{knitrout}
 864 | 
 865 | 
 866 | Then just call your function to generate a plot.
 867 | It's a lot easier to fix one function that do it over and over for many plots
 868 | \begin{knitrout}\footnotesize
 869 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 870 | \begin{alltt}
 871 | \hlstd{plot1} \hlkwb{<-} \hlkwd{my_custom_plot}\hlstd{(dataset1,} \hlkwc{title} \hlstd{=} \hlstr{"Figure 1"}\hlstd{)}
 872 | \end{alltt}
 873 | \end{kframe}
 874 | \end{knitrout}
 875 | 
 876 | 
 877 | 
 878 | \end{frame}
 879 | 
 880 | % --------------------------------------------------------------
 881 | \section*{Scales}
 882 | \frame{\sectionpage}
 883 | 
 884 | % --------------------------------------------------------------
 885 | \begin{frame}[fragile]
 886 | \frametitle{Commonly used scales}
 887 | \begin{knitrout}\footnotesize
 888 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 889 | \begin{alltt}
 890 | \hlkwd{scale_fill_discrete}\hlstd{();} \hlkwd{scale_colour_discrete}\hlstd{()}
 891 | \hlkwd{scale_fill_hue}\hlstd{();} \hlkwd{scale_color_hue}\hlstd{()}
 892 | \hlkwd{scale_fill_manual}\hlstd{();}  \hlkwd{scale_color_manual}\hlstd{()}
 893 | \hlkwd{scale_fill_brewer}\hlstd{();} \hlkwd{scale_color_brewer}\hlstd{()}
 894 | \hlkwd{scale_linetype}\hlstd{();} \hlkwd{scale_shape_manual}\hlstd{()}
 895 | \end{alltt}
 896 | \end{kframe}
 897 | \end{knitrout}
 898 | 
 899 | \end{frame}
 900 | 
 901 | % --------------------------------------------------------------
 902 | \begin{frame}[fragile]
 903 | \frametitle{Adding a continuous scale}
 904 | \begin{knitrout}\footnotesize
 905 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 906 | \begin{alltt}
 907 | \hlkwd{library}\hlstd{(MASS)}
 908 | \hlkwd{ggplot}\hlstd{(birthwt,} \hlkwd{aes}\hlstd{(}\hlkwd{factor}\hlstd{(race), bwt))} \hlopt{+}
 909 | \hlkwd{geom_boxplot}\hlstd{(}\hlkwc{width} \hlstd{=} \hlnum{.2}\hlstd{)} \hlopt{+}
 910 | \hlkwd{scale_y_continuous}\hlstd{(}\hlkwc{labels} \hlstd{= (}\hlkwd{paste0}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{4}\hlstd{,} \hlstr{" Kg"}\hlstd{)),}
 911 | \hlkwc{breaks} \hlstd{=} \hlkwd{seq}\hlstd{(}\hlnum{1000}\hlstd{,} \hlnum{4000}\hlstd{,} \hlkwc{by} \hlstd{=} \hlnum{1000}\hlstd{))}
 912 | \end{alltt}
 913 | \end{kframe}
 914 | \includegraphics[width=.75\linewidth]{figure/boxplots3_} 
 915 | 
 916 | \end{knitrout}
 917 | 
 918 | \end{frame}
 919 | 
 920 | 
 921 | % --------------------------------------------------------------
 922 | \begin{frame}[fragile]
 923 | \frametitle{Another continuous scale with custom labels}
 924 | \begin{knitrout}\footnotesize
 925 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 926 | \begin{alltt}
 927 | \hlcom{# Assign the plot to an object}
 928 | \hlstd{dd} \hlkwb{<-} \hlkwd{ggplot}\hlstd{(iris,} \hlkwd{aes}\hlstd{(Sepal.Length, Sepal.Width,} \hlkwc{color} \hlstd{= Species))} \hlopt{+}
 929 | \hlkwd{geom_point}\hlstd{(}\hlkwc{size} \hlstd{=} \hlnum{4}\hlstd{,} \hlkwc{shape} \hlstd{=} \hlnum{16}\hlstd{)} \hlopt{+}
 930 | \hlkwd{facet_grid}\hlstd{(.} \hlopt{~}\hlstd{Species)}
 931 | \hlcom{# Now add a scale}
 932 | \hlstd{dd} \hlopt{+}
 933 | \hlkwd{scale_y_continuous}\hlstd{(}\hlkwc{breaks} \hlstd{=} \hlkwd{seq}\hlstd{(}\hlnum{2}\hlstd{,} \hlnum{8}\hlstd{,} \hlkwc{by} \hlstd{=} \hlnum{1}\hlstd{),}
 934 | \hlkwc{labels} \hlstd{=} \hlkwd{paste0}\hlstd{(}\hlnum{2}\hlopt{:}\hlnum{8}\hlstd{,} \hlstr{" cm"}\hlstd{))}
 935 | \end{alltt}
 936 | \end{kframe}
 937 | \end{knitrout}
 938 | 
 939 | \end{frame}
 940 | 
 941 | 
 942 | % --------------------------------------------------------------
 943 | \begin{frame}[fragile]
 944 | \frametitle{gradients}
 945 | \begin{knitrout}\footnotesize
 946 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 947 | \begin{alltt}
 948 | \hlstd{h} \hlopt{+} \hlkwd{geom_histogram}\hlstd{(} \hlkwd{aes}\hlstd{(}\hlkwc{fill} \hlstd{= ..count..),} \hlkwc{color}\hlstd{=}\hlstr{"black"}\hlstd{)} \hlopt{+}
 949 | \hlkwd{scale_fill_gradient}\hlstd{(}\hlkwc{low}\hlstd{=}\hlstr{"green"}\hlstd{,} \hlkwc{high}\hlstd{=}\hlstr{"red"}\hlstd{)}
 950 | \end{alltt}
 951 | \end{kframe}
 952 | \includegraphics[width=.75\linewidth]{figure/scale_2} 
 953 | 
 954 | \end{knitrout}
 955 | 
 956 | \end{frame}
 957 | 
 958 | 
 959 | 
 960 | % --------------------------------------------------------------
 961 | \section*{Publication quality figures}
 962 | \frame{\sectionpage}
 963 | 
 964 | % How to save your plots
 965 | % --------------------------------------------------------------
 966 | \begin{frame}[fragile]
 967 | \begin{itemize}
 968 | \item If the plot is on your screen
 969 | \begin{knitrout}\footnotesize
 970 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 971 | \begin{alltt}
 972 | \hlkwd{ggsave}\hlstd{(}\hlstr{"~/path/to/figure/filename.png"}\hlstd{)}
 973 | \end{alltt}
 974 | \end{kframe}
 975 | \end{knitrout}
 976 | 
 977 | \item If your plot is assigned to an object
 978 | \begin{knitrout}\footnotesize
 979 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 980 | \begin{alltt}
 981 | \hlkwd{ggsave}\hlstd{(plot1,} \hlkwc{file} \hlstd{=} \hlstr{"~/path/to/figure/filename.png"}\hlstd{)}
 982 | \end{alltt}
 983 | \end{kframe}
 984 | \end{knitrout}
 985 | 
 986 | 
 987 | \item Specify a size
 988 | \begin{knitrout}\footnotesize
 989 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
 990 | \begin{alltt}
 991 | \hlkwd{ggsave}\hlstd{(}\hlkwc{file} \hlstd{=} \hlstr{"/path/to/figure/filename.png"}\hlstd{,} \hlkwc{width} \hlstd{=} \hlnum{6}\hlstd{,}
 992 | \hlkwc{height} \hlstd{=}\hlnum{4}\hlstd{)}
 993 | \end{alltt}
 994 | \end{kframe}
 995 | \end{knitrout}
 996 | 
 997 | \item or any format (pdf, png, eps, svg, jpg)
 998 | \begin{knitrout}\footnotesize
 999 | \definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
1000 | \begin{alltt}
1001 | \hlkwd{ggsave}\hlstd{(}\hlkwc{file} \hlstd{=} \hlstr{"/path/to/figure/filename.eps"}\hlstd{)}
1002 | \hlkwd{ggsave}\hlstd{(}\hlkwc{file} \hlstd{=} \hlstr{"/path/to/figure/filename.jpg"}\hlstd{)}
1003 | \hlkwd{ggsave}\hlstd{(}\hlkwc{file} \hlstd{=} \hlstr{"/path/to/figure/filename.pdf"}\hlstd{)}
1004 | \end{alltt}
1005 | \end{kframe}
1006 | \end{knitrout}
1007 | 
1008 | \end{itemize}
1009 | \end{frame}
1010 | 
1011 | % --------------------------------------------------------------
1012 | \begin{frame}[fragile]
1013 | \frametitle{Further help}
1014 | \begin{itemize}
1015 | \item You've just scratched the surface with ggplot2.
1016 | \item Practice
1017 | \item Read the docs (either locally in \texttt{R} or at \url{http://docs.ggplot2.org/current/})
1018 | \item Work together
1019 | \end{itemize}
1020 | \includegraphics[scale=.15]{images/chang_book.png}
1021 | \includegraphics[scale=.15]{images/hadley.png}
1022 | \end{frame}
1023 | 
1024 | % --------------------------------------------------------------
1025 | % end, hope it was useful.
1026 | \end{document}
1027 | 


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/images/hadley.png:
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https://raw.githubusercontent.com/karthik/ggplot-lecture/b2980ab6df3dc2053d3e7c46db44616d3db9c0c7/images/hadley.png


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/make.sh:
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 1 | 
 2 | cd ~/Github/ggplot2-lecture/
 3 | rm ggplot.tex
 4 | Rscript -e "library(knitr); knit('ggplot.Rnw', quiet = TRUE)"
 5 | pdflatex ggplot.tex
 6 | open ggplot.pdf
 7 | rm *.log
 8 | rm *.nav
 9 | rm *.out
10 | rm *.snm
11 | rm *.toc
12 | rm *.vrb
13 | # added a comment.
14 | 


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/slides.png:
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