-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathdataviz.html
582 lines (496 loc) · 21 KB
/
dataviz.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Data visualization / Visualisation de données</title>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
<link href="site_libs/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-5.1.3/bootstrap.bundle.min.js"></script>
<script src="site_libs/bs3compat-0.4.0/transition.js"></script>
<script src="site_libs/bs3compat-0.4.0/tabs.js"></script>
<script src="site_libs/bs3compat-0.4.0/bs3compat.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
</head>
<body>
<div class="container-fluid main-container">
<div class="navbar navbar-dark navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"></a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
</a>
</li>
<li>
<a href="publications.html">Recherche - Research</a>
</li>
<li>
<a href="teaching.html">Enseignement - Teaching</a>
</li>
<li>
<a href="datasets.html">Données - Data</a>
</li>
<li>
<a href="dataviz.html">Dataviz</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="mailto:florence.vallee-dubois@umontreal.ca">
<span class="fa fa-envelope-o"></span>
</a>
</li>
<li>
<a href="https://github.com/florencevdubois">
<span class="fa fa-github"></span>
</a>
</li>
<li>
<a href="https://twitter.com/florencevdubois">
<span class="fa fa-twitter"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<div class="btn-group pull-right float-right">
<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
</div>
<h1 class="title toc-ignore">Data visualization / Visualisation de
données</h1>
</div>
<p><br> <br></p>
<div id="tidy-tuesdays" class="section level2 tabset">
<h2 class="tabset">Tidy Tuesdays</h2>
<p>Below, you will find some of the graphs (and accompanying code) I
made as part of the <a href="https://twitter.com/R4DScommunity">R4DS</a>
weekly visualization challenges. All of the entries I made for
#TidyTuesday can be found on my <a
href="https://github.com/florencevdubois/MyTidyTuesdays">Github</a>
page.</p>
<div id="february-2020" class="section level3">
<h3>25 February 2020</h3>
<p>On this week’s TidyTuesday challenge, we worked with data on
vaccination rates across the USA. I decided to make a graph of
vaccination rates by county. See below for the final product. Start by
loading the necessary packages and the measles data.</p>
<pre class="r"><code># packages
library(tidyverse)
library(pacman)
library(tidyverse)
# data
measles <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2020/2020-02-25/measles.csv')</code></pre>
<p>Let’s explore the data.</p>
<pre class="r"><code>summary(measles$mmr) # distribution of vaccination rates
summary(measles$overall) # distribution of vaccination rates
weird <- measles %>%
filter(overall == -1 | mmr == -1)# who are the "-1" ? Apparently they're missing data.
table(weird$state) # some have missing data for "mmr", some have missing data for "overall" -- we will use this later
length(unique(measles$county)) # how many unique counties?
table(measles$year, useNA = "always") # which years?</code></pre>
<p>Then, we need to do some data clean-up.</p>
<pre class="r"><code>measles_plot_viz <- measles %>%
distinct(state, name, county, overall, mmr, lat, lng, enroll) %>% # remove duplicates
mutate(drop = ifelse(mmr >= 0 & overall >= 0, "drop", "keep")) %>%
filter(lng < 0) %>% # remove schools outside of the continent
gather(type, value, overall:mmr) %>%
filter(value >= 0) %>%
filter(!(drop == "drop" & type == "overall"))</code></pre>
<p>Finally, let’s draw the map! I will be using the <code>maps</code>
package to do so. I had help from Kieran Healy’s <a
href="https://socviz.co/maps.html#maps">book</a> during this step, as
well as Timo Grossenbacher’s <a
href="https://timogrossenbacher.ch/2016/12/beautiful-thematic-maps-with-ggplot2-only/">blog</a>.</p>
<pre class="r"><code># load packages
library(maps)
library(mapproj)
# 1. load the county data
us_counties <- map_data("county") %>%
mutate(state_county = str_c(region, subregion, sep = "_"))
head(us_counties)
# 2. check the distribution of vacc. rate
summary(measles_plot_viz$value)
# 3. draw a plain county map to see if it's working
p <- ggplot(mapping = aes(x = long, y = lat, group = group), data = us_counties)
p1 <- p + geom_polygon(color = "white", size = 0.1) +
coord_map(projection = "albers", lat0 = 39, lat1 = 45) +
guides(fill = FALSE) +
theme_minimal()</code></pre>
<pre><code>## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.</code></pre>
<pre class="r"><code>p1</code></pre>
<p><img src="dataviz_files/figure-html/unnamed-chunk-4-1.png" width="672" /></p>
<p>Now that we know the map is working at the vaccination data makes
sense, we can plot vaccination rates across the U.S. But first, for the
map’s caption, we need to check which type of vaccination rate is
plotted in which state:</p>
<pre class="r"><code>table(measles_plot_viz$type, measles_plot_viz$state) </code></pre>
<pre><code>##
## Arizona Arkansas California Colorado Connecticut Florida Idaho
## mmr 1171 567 14068 1501 586 0 0
## overall 0 0 0 0 0 2667 467
##
## Illinois Iowa Maine Massachusetts Michigan Minnesota Missouri
## mmr 7115 0 357 946 0 1570 645
## overall 0 1163 0 0 2351 0 0
##
## Montana New Jersey New York North Carolina North Dakota Ohio
## mmr 520 0 4137 0 360 2919
## overall 0 1993 0 2083 0 0
##
## Oklahoma Oregon Pennsylvania Rhode Island South Dakota Tennessee
## mmr 0 806 1930 0 373 0
## overall 1052 0 0 215 0 1152
##
## Texas Utah Vermont Washington Wisconsin
## mmr 810 603 255 1977 0
## overall 0 0 0 0 2497</code></pre>
<p>Now we can plot:</p>
<pre class="r"><code># 4. draw map with vacc. data
p <- ggplot()
p1 <- p +
geom_polygon(mapping = aes(x = long, y = lat, group = group),
data = us_counties,
fill = "#f5f5f2",
color = "black",
size = 0.1) + # add county lines
geom_point(mapping = aes(x = lng, y = lat, color = value),
data = subset(measles_plot_viz, value > 50),
size = 0.6) + # add school dots
coord_map(projection = "albers", lat0 = 39, lat1 = 45) + # make the map more "curvy"
theme_void() + # remove grid and axes
theme(legend.position = "bottom",
plot.title = element_text(hjust = 0.5,
vjust = 0.5,
size = 15),
plot.background = element_rect(fill = "#f5f5f2",
color = NA),
plot.caption = element_text(hjust = 0.5,
size = 10),
plot.margin = margin(t = 1, r = 1, b = 1, l = 1,
unit = "cm"),
legend.margin = margin(t = 2, r = 2, b = 5, l = 2,
unit = "mm")) + # modify plot title/caption/background/legend
scale_color_viridis_c(option = "plasma",
direction = -1,
name = "Vaccination rate",
guide = guide_legend(direction = "horizontal",
title.position = "top",
title.hjust = 0.5)) + # change legend title
labs(title = "Schools' Vaccination Rate in 31 U.S. States",
caption = "Measles, Mumps, and Rubella (MMR) vaccination\nrate shown in FL, ID, IA, MI, NJ, NC, OK, RI, TN, WI.\nElsewhere, the overall vaccination rate is shown.") # deifne title and subtitle
p1</code></pre>
<p><img src="dataviz_files/figure-html/unnamed-chunk-6-1.png" width="1440" /></p>
<pre class="r"><code># save plot using ggsave(filename = "name.png", plot = last_plot(), width = 15, height = 15)</code></pre>
</div>
<div id="june-2020" class="section level3">
<h3>9 June 2020</h3>
<p>For this week,s TidyTuesday, I create a graph that reports the names
and achievements of African-Americans in the Arts and Entertainment. I
chose a bar chart, where each bar corresponds to a decade of
African-American accomplishments. Start by loading the necessary
packages and the data on African-American firsts.</p>
<pre class="r"><code>library(tidyverse)
library(extrafont)
firsts <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2020/2020-06-09/firsts.csv')
# Let's explore some variables
table(firsts$category)</code></pre>
<p>Now, we will recode the data. We will focus on the
<code>person</code> variable, which contains the information on who the
achiever is, and what they’ve accomplished. Once we’ve cleaned up the
<code>person</code> variable, we will create a categorical variable for
the decade of achievement, and collapse everyone (and their
accomplishment) from the same decade together into one observation. The
last thing we will do is insert a new line every 20 characters. If we do
not insert the new line, the text will run too wide in the graph.</p>
<pre class="r"><code>dat <- firsts %>%
mutate(person_sh = str_remove_all(person, "\\(.*\\)"), # remove everything in parenthesis
person_sh = str_remove_all(person, "\\(.*"), # remove everything in parenthesis
person_sh = str_remove_all(person_sh, "\\[.*\\]"), # remove brackets and their content
person_sh = str_trim(person_sh, "right"), # remove white space at the end of names
person_complete = str_c(person_sh, ", ", accomplishment), # create complete name + accomplishment title
word_count = str_count(person_complete), # count number of words in complete names
count = 1,
person_complete = str_replace_all(person_complete, "African-American", "Af-Am"), # shorten for visualization purposes
twenty_yr = ifelse(year <= 1780, '1760s-70s',
ifelse(year >= 1781 & year <= 1800, "1780s-90s",
ifelse(year >= 1801 & year <= 1820, "1800s-10s",
ifelse(year >= 1821 & year <= 1840, "1820s-30s",
ifelse(year >= 1841 & year <= 1860, "1840s-50s",
ifelse(year >= 1861 & year <= 1880, "1860s-70s",
ifelse(year >= 1881 & year <= 1900, "1880s-90s",
ifelse(year >= 1901 & year <= 1920, "1900s-10s",
ifelse(year >= 1921 & year <= 1940, "1920s-30s",
ifelse(year >= 1941 & year <= 1960, "1940s-50s",
ifelse(year >= 1961 & year <= 1980, "1960s-70s",
ifelse(year >= 1981 & year <= 2000, "1980s-90s", "2000s-10s"))))))))))))) %>% # create categorical variable for twenty years
group_by(twenty_yr, category) %>%
mutate(persons_20 = paste0(person_complete, collapse = "; ")) %>% # collapse strings for each twenty years and category
ungroup() %>%
group_by(category) %>%
mutate(count_cat = cumsum(count)) %>%
ungroup() %>%
distinct(twenty_yr, count_cat, category, persons_20) %>%
group_by(twenty_yr, category) %>%
arrange(count_cat) %>%
filter(row_number() == n())
dat$persons_20 <- gsub("(.{15,}?)\\s", "\\1\n", dat$persons_20) # insert new line every 15 characters</code></pre>
<p>Let’s make the graph! I was inspired by G. Karamanis’s work to do
this graph. You can check out his work <a
href="https://github.com/gkaramanis/tidytuesday/blob/master/2020-week23/marbles-race.R">here</a>.
I decided to plot accomplishments in the Arts and Entertainment only,
but you could do the same with science, education, sports, etc.</p>
<pre class="r"><code># plot, Arts only
viz <- dat %>% filter(category == "Arts & Entertainment")
p <- ggplot(viz, aes(x = twenty_yr, y = count_cat))
p1 <- p +
scale_y_continuous(name = "",
limits = c(-700,700)) +
scale_x_discrete(name = "",
expand = c(0.2, 0)) +
annotate("text", x = viz$twenty_yr, # add names
y = viz$count_cat,
label = viz$persons_20,
size = 2.5,
color = "white",
family = "Arial Narrow") +
annotate("text", x = "1760s-70s", # add title
y = 400,
label = "First\nAfrican Americans\nin Arts & Entertainment",
size = 15,
hjust = 0,
color = "white",
family = "Andale Mono") +
theme_void() +
coord_cartesian(clip = "off") +
theme(plot.background = element_rect(fill = 'grey11', colour = 'grey11'),
plot.margin = margin(200, 40, 100, 30), # play with margins
axis.text.x = element_text(colour = "gray69", # modify x axis
size = 15,
family = "Andale Mono"))
p1</code></pre>
<p><img src="dataviz_files/figure-html/unnamed-chunk-9-1.png" width="1920" /></p>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
window.initializeCodeFolding("show" === "show");
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>