Attachment 'LSA13-Lecture5-ggplot.R'
Download 1 ## @knitr Options, include=F, cache=F, message=F
2 opts_chunk$set(size='footnotesize', eval=T, cache=T, prompt=F, message=F, tidy=F)
3
4
5 ## @knitr gettinstarted, echo=T, results='hide', cache=T, message=F, size='normalsize'
6 library(ggplot2)
7 library(languageR)
8 library(Hmisc)
9 data(lexdec)
10
11 # define some functions
12 se <- function(x)
13 {
14 y <- x[!is.na(x)] # remove the missing values, if any
15 sqrt(var(as.vector(y))/length(y))
16 }
17
18
19 ## @knitr histogram1, echo=T, results='hide', cache=T, message=F, size='normalsize',out.width='.5\\textwidth',fig.align='center'
20 # Create a histogram of RTs in the lexdec dataset
21 ggplot(lexdec, aes(x=RT)) +
22 geom_histogram()
23
24
25 ## @knitr histogram2, echo=F, results='hide', cache=T, message=F, size='normalsize',out.width='.5\\textwidth',fig.align='center'
26 ggplot(lexdec, aes(x=RT)) +
27 geom_histogram(binwidth=0.02)
28
29
30 ## @knitr histogram3, echo=T, results='hide', cache=T, message=F, size='normalsize',out.width='.5\\textwidth',eval=FALSE
31 ## ggplot(lexdec, aes(x=RT)) +
32 ## geom_histogram(binwidth=0.02)
33
34
35 ## @knitr density1, echo=F, results='hide', cache=T, message=F, size='normalsize',out.width='.5\\textwidth',fig.align='center'
36 ggplot(lexdec, aes(x=RT)) +
37 geom_density()
38
39
40 ## @knitr density2, echo=T, results='hide', cache=T, message=F, size='normalsize',eval=FALSE
41 ## ggplot(lexdec, aes(x=RT)) +
42 ## geom_density()
43
44
45 ## @knitr dh1, echo=F, results='hide', cache=T, message=F, size='normalsize',out.width='.5\\textwidth',fig.align='center'
46 ggplot(lexdec, aes(x=RT)) +
47 geom_histogram(aes(y = ..density..)) +
48 geom_density()
49
50
51 ## @knitr dh2, echo=T, results='hide', cache=T, message=F, size='normalsize',eval=FALSE
52 ## ggplot(lexdec, aes(x=RT)) +
53 ## geom_histogram(aes(y = ..density..)) +
54 ## geom_density()
55
56
57 ## @knitr facet1, echo=F, results='hide', cache=T, message=F, size='normalsize',fig.width=6, out.width='.8\\textwidth',fig.align='center'
58 ggplot(lexdec, aes(x=RT)) +
59 geom_density() +
60 facet_wrap( ~ Subject,nrow=4)
61
62
63 ## @knitr facet2, echo=T, results='hide', cache=T, message=F, size='normalsize',eval=FALSE
64 ## ggplot(lexdec, aes(x=RT)) +
65 ## geom_density() +
66 ## facet_wrap( ~ Subject,nrow=4)
67
68
69 ## @knitr color2, echo=T, results='hide', cache=T, message=F, size='small',fig.width=6, out.width='\\textwidth',fig.align='center'
70 ggplot(lexdec, aes(x=RT)) +
71 geom_histogram(fill="green")
72
73
74 ## @knitr color1, echo=T, results='hide', cache=T, message=F, size='small',fig.width=6, out.width='\\textwidth',fig.align='center'
75 ggplot(lexdec, aes(x=RT,fill="green")) +
76 geom_histogram()
77
78
79 ## @knitr nl1, echo=F, results='hide', cache=T, message=F, size='normalsize',fig.width=6, out.width='.6\\textwidth',fig.align='center'
80 ggplot(lexdec, aes(x=RT, color=NativeLanguage)) +
81 geom_density()
82
83
84 ## @knitr nl2, echo=T, results='hide', cache=T, message=F, size='normalsize',eval=FALSE
85 ## ggplot(lexdec, aes(x=RT, color=NativeLanguage)) +
86 ## geom_density()
87
88
89 ## @knitr agr, echo=T, results='markup', cache=T, size='small'
90 agr = aggregate(RT ~ NativeLanguage,
91 lexdec, mean)
92 agr
93
94
95 ## @knitr bar1, echo=F, results='hide', fig.width=4, out.width='.6\\textwidth',fig.align='center'
96 ggplot(agr, aes(x=NativeLanguage,y=RT)) +
97 geom_bar(stat="identity")
98
99
100 ## @knitr bar2, echo=T, results='hide', eval=FALSE
101 ## ggplot(agr, aes(x=NativeLanguage,y=RT)) +
102 ## geom_bar(stat="identity")
103
104
105 ## @knitr bar3, echo=F, results='hide', fig.width=6, out.width='.6\\textwidth',fig.align='center'
106 agr = aggregate(RT ~ NativeLanguage + Class, lexdec, mean)
107 ggplot(agr, aes(x=NativeLanguage, y=RT, fill=Class)) +
108 geom_bar(stat="identity",position="dodge")
109
110
111 ## @knitr bar4, echo=T, results='hide', cache=T, message=F, eval=FALSE
112 ## ggplot(agr, aes(x=NativeLanguage, y=RT, fill=Class)) +
113 ## geom_bar(stat="identity",position="dodge")
114
115
116 ## @knitr errbar0, echo=F, results='hide'
117 agr = aggregate(RT ~ NativeLanguage +
118 Class, lexdec, mean)
119 agr$SE = aggregate(RT ~ NativeLanguage
120 + Class, lexdec, se)$RT
121 agr$YMin = agr$RT - agr$SE
122 agr$YMax = agr$RT + agr$SE
123
124
125 ## @knitr errbar2, echo=F, results='hide', out.width='.7\\textwidth', fig.width=4, fig.align='center'
126 ggplot(agr, aes(x=NativeLanguage, y=RT, fill=Class)) +
127 geom_bar(stat="identity",position="dodge") +
128 geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25)
129
130
131 ## @knitr errbar1, eval=F
132 agr = aggregate(RT ~ NativeLanguage +
133 Class, lexdec, mean)
134 agr$SE = aggregate(RT ~ NativeLanguage
135 + Class, lexdec, se)$RT
136 agr$YMin = agr$RT - agr$SE
137 agr$YMax = agr$RT + agr$SE
138
139
140 ## @knitr errbar3, results='hide', fig.width=6, out.width='.7\\textwidth',fig.align='center', eval=FALSE
141 ## ggplot(agr, aes(x=NativeLanguage, y=RT, fill=Class)) +
142 ## geom_bar(stat="identity", position="dodge") +
143 ## geom_errorbar(aes(ymin=YMin, ymax=YMax),width=0.25)
144 ##
145
146
147 ## @knitr errbar4, echo=T, results='hide', cache=T, message=F, size='normalsize',fig.width=6, out.width='.5\\textwidth',fig.align='center'
148 dodge = position_dodge(.9)
149 ggplot(agr, aes(x=NativeLanguage, y=RT, fill=Class)) +
150 geom_bar(stat="identity",position=dodge) +
151 geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25,position=dodge)
152
153
154
155 ## @knitr errbar5b, echo=T, results='hide',fig.width=6, out.width='.5\\textwidth',fig.align='center'
156 ggplot(agr, aes(x=NativeLanguage, y=RT, fill=Class)) +
157 geom_bar(stat="identity",position=dodge) +
158 geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25,position=dodge) +
159 coord_cartesian(ylim=c(6,6.6))
160
161
162 ## @knitr errbar6, echo=F, results='hide', fig.width=6, out.width='.5\\textwidth',fig.align='center'
163 ggplot(agr, aes(x=NativeLanguage, y=RT, color=Class)) +
164 geom_point(position=dodge) +
165 geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25,position=dodge) +
166 coord_cartesian(ylim=c(6.2,6.6))
167
168
169 ## @knitr errbar7, echo=T, results='hide',fig.width=6, out.width='.5\\textwidth',fig.align='center',eval=FALSE
170 ## ggplot(agr, aes(x=NativeLanguage, y=RT, color=Class)) +
171 ## geom_point(position=dodge) +
172 ## geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25,position=dodge) +
173 ## coord_cartesian(ylim=c(6.2,6.6))
174
175
176 ## @knitr errbar8, echo=F, results='hide'
177 library(bootstrap)
178 theta <- function(x,xdata,na.rm=T) {mean(xdata[x],na.rm=na.rm)}
179 ci.low <- function(x,na.rm=T) {
180 mean(x,na.rm=na.rm) - quantile(bootstrap(1:length(x),1000,theta,x,na.rm=na.rm)$thetastar,.025,na.rm=na.rm)}
181 ci.high <- function(x,na.rm=T) {
182 quantile(bootstrap(1:length(x),1000,theta,x,na.rm=na.rm)$thetastar,.975,na.rm=na.rm) - mean(x,na.rm=na.rm)}
183
184 agrr = aggregate(RT ~ NativeLanguage + Class + Subject, data=lexdec, mean)
185 agr = aggregate(RT ~ NativeLanguage + Class, data=agrr, mean)
186 agr$CIH = aggregate(RT ~ NativeLanguage + Class, data=agrr, FUN=ci.high)$RT
187 agr$CIL = aggregate(RT ~ NativeLanguage + Class, data=agrr, FUN=ci.low)$RT
188 agr$YMin = agr$RT - agr$CIL
189 agr$YMax = agr$RT + agr$CIH
190
191
192 ## @knitr errbar9, echo=F, results='hide',fig.width=6, out.width='\\textwidth',fig.align='center'
193 ggplot(agr, aes(x=NativeLanguage, y=RT, color=Class)) +
194 geom_point(position=dodge) +
195 geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25,position=dodge) +
196 scale_y_continuous(limits=c(6,6.75))
197
198
199 ## @knitr errbar10, ,eval=F
200 agrr = aggregate(RT ~ NativeLanguage +
201 Class + Subject, lexdec, mean)
202 agr = aggregate(RT ~ NativeLanguage +
203 Class, agrr, mean)
204 agr$CIH = aggregate(RT ~ NativeLanguage +
205 Class, agrr, ci.high)$RT
206 agr$CIL = aggregate(RT ~ NativeLanguage +
207 Class, agrr, ci.low)$RT
208 agr$YMin = agr$RT - agr$CIL
209 agr$YMax = agr$RT + agr$CIH
210
211
212 ## @knitr errbar11, results='hide', fig.width=6, out.width='.9\\textwidth',fig.align='center',eval=FALSE
213 ## ggplot(agr, aes(x=NativeLanguage, y=RT, color=Class)) +
214 ## geom_point(position=dodge) +
215 ## geom_errorbar(aes(ymin=YMin,ymax=YMax),width=0.25,
216 ## position=dodge) +
217 ## scale_y_continuous(limits=c(6,6.75))
218 ##
219 ##
220
221
222 ## @knitr sp1, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
223 ggplot(lexdec, aes(x=Frequency, y=RT)) +
224 geom_point()
225
226
227 ## @knitr sp2, results='hide', eval=FALSE
228 ## ggplot(lexdec, aes(x=Frequency, y=RT)) +
229 ## geom_point()
230
231
232 ## @knitr jitter1, echo=F, results='hide',fig.width=6, out.width='.45\\textwidth',fig.align='center'
233 ggplot(lexdec, aes(x=Frequency, y=RT)) +
234 geom_jitter(position = position_jitter(width = 0.1, height=0.1))
235
236
237
238 ## @knitr jitter2, results='hide', eval=FALSE
239 ## ggplot(lexdec, aes(x=Frequency, y=RT)) +
240 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1))
241 ##
242
243
244 ## @knitr lowess11, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth', fig.align='center'
245 ggplot(lexdec, aes(x=Frequency, y=RT)) +
246 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
247 stat_smooth()
248
249
250
251 ## @knitr lowess12, results='hide', eval=FALSE
252 ## ggplot(lexdec, aes(x=Frequency, y=RT)) +
253 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
254 ## stat_smooth()
255 ##
256
257
258 ## @knitr linear1, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
259 ggplot(lexdec, aes(x=Frequency, y=RT)) +
260 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
261 stat_smooth(method="lm")
262
263
264 ## @knitr linear2, results='hide', eval=FALSE
265 ## ggplot(lexdec, aes(x=Frequency, y=RT)) +
266 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
267 ## stat_smooth(method="lm")
268
269
270 ## @knitr sp3, echo=F, results='hide',fig.width=6, out.width='.45\\textwidth',fig.align='center'
271 ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
272 geom_jitter(position = position_jitter(width = 0.1, height=0.1))
273
274
275
276 ## @knitr sp4, results='hide', eval=FALSE
277 ## ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
278 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1))
279 ##
280
281
282 ## @knitr shape1, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
283 ggplot(lexdec, aes(x=Frequency, y=RT, shape=NativeLanguage)) +
284 geom_jitter(position = position_jitter(width = 0.1, height=0.1))
285
286
287
288 ## @knitr shape2, results='hide', eval=FALSE
289 ## ggplot(lexdec, aes(x=Frequency, y=RT, shape=NativeLanguage)) +
290 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1))
291 ##
292
293
294 ## @knitr shapec1, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
295 ggplot(lexdec, aes(x=Frequency, y=RT, shape=NativeLanguage,
296 color=NativeLanguage)) +
297 geom_jitter(position = position_jitter(width = 0.1, height=0.1))
298
299
300
301 ## @knitr shapec2, results='hide', eval=FALSE
302 ## ggplot(lexdec, aes(x=Frequency, y=RT, shape=NativeLanguage, color=NativeLanguage)) +
303 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1))
304 ##
305
306
307 ## @knitr sm1, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
308 ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
309 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
310 stat_smooth(method="lm")
311
312
313
314 ## @knitr sm2, results='hide', eval=FALSE
315 ## ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
316 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
317 ## stat_smooth(method="lm")
318 ##
319
320
321 ## @knitr binfs1, echo=F, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
322 ggplot(lexdec, aes(x=Frequency, y=RT, color=cut2(FamilySize,g=3))) +
323 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
324 stat_smooth(method="lm")
325
326
327
328 ## @knitr cut
329 table(cut(lexdec$FamilySize,breaks=3))
330 table(cut2(lexdec$FamilySize,g=3))
331
332
333 ## @knitr binfs2, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
334 ggplot(lexdec, aes(x=Frequency, y=RT, color=cut2(FamilySize,g=3))) +
335 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
336 stat_smooth(method="lm")
337
338
339
340 ## @knitr text1, results='hide', fig.width=8, fig.height=5, out.width='.75\\textwidth',fig.align='center'
341 agr = aggregate(RT ~ Word + Frequency, lexdec, mean)
342 ggplot(agr, aes(x=Frequency, y=RT)) +
343 geom_point() +
344 geom_text(aes(label=Word),vjust=1)
345
346
347
348 ## @knitr app1, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
349 ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
350 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
351 stat_smooth(method="lm") +
352 scale_x_continuous(name="Log-transformed word frequency")
353
354
355 ## @knitr theme1, results='hide', fig.width=6, out.width='.45\\textwidth',fig.align='center'
356 ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
357 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
358 stat_smooth(method="lm") +
359 theme(axis.text.x=element_text(size=12,color="blue"))
360
361
362 ## @knitr theme2, echo=F, results='hide',fig.width=5, fig.height=4.5,out.width='\\textwidth',fig.align='center'
363 ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
364 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
365 stat_smooth(method="lm") +
366 theme(axis.text=element_text(size=12), axis.title=element_text(color="red"), legend.position="top")
367
368
369 ## @knitr theme3, results='hide', eval=FALSE
370 ## ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
371 ## geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
372 ## stat_smooth(method="lm") +
373 ## theme(axis.text=element_text(size=12), axis.title=
374 ## element_text(color="red"), legend.position="top")
375
376
377 ## @knitr theme4, results='hide', fig.width=6,out.width='.45\\textwidth',fig.align='center'
378 theme_set(theme_bw())
379 ggplot(lexdec, aes(x=Frequency, y=RT, color=NativeLanguage)) +
380 geom_jitter(position = position_jitter(width = 0.1, height=0.1)) +
381 stat_smooth(method="lm") +
382 theme(axis.text=element_text(size=12), axis.title=
383 element_text(color="red"))
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