-
Notifications
You must be signed in to change notification settings - Fork 29
/
ff_plot.html
244 lines (194 loc) · 11.6 KB
/
ff_plot.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
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Produce a table and plot — ff_plot • finalfit</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Produce a table and plot — ff_plot" />
<meta property="og:description" content="Wraps or_plot, hr_plot, and
coefficient_plot and sends to the appropriate method depending
on the dependent variable type." />
<meta property="og:image" content="/logo.png" />
<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default 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" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">finalfit</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.1</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa fas fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../articles/finalfit.html">Get started</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/all_tables_examples.html">All tables examples</a>
</li>
<li>
<a href="../articles/bootstrap.html">Bootstrap simulation for model prediction</a>
</li>
<li>
<a href="../articles/data_prep.html">Preparing data for finalfit</a>
</li>
<li>
<a href="../articles/export.html">Exporting tables and plots</a>
</li>
<li>
<a href="../articles/missing.html">Missing data</a>
</li>
<li>
<a href="../articles/survival.html">Time-to-event (Survival)</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/ewenharrison/finalfit">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Produce a table and plot</h1>
<small class="dont-index">Source: <a href='https://github.com/ewenharrison/finalfit/blob/master/R/ff_plot.R'><code>R/ff_plot.R</code></a></small>
<div class="hidden name"><code>ff_plot.Rd</code></div>
</div>
<div class="ref-description">
<p>Wraps <code><a href='or_plot.html'>or_plot</a></code>, <code><a href='hr_plot.html'>hr_plot</a></code>, and
<code><a href='coefficient_plot.html'>coefficient_plot</a></code> and sends to the appropriate method depending
on the dependent variable type.</p>
</div>
<pre class="usage"><span class='fu'>ff_plot</span>(<span class='no'>.data</span>, <span class='no'>dependent</span>, <span class='no'>explanatory</span>, <span class='no'>...</span>)
<span class='fu'>finalfit_plot</span>(<span class='no'>.data</span>, <span class='no'>dependent</span>, <span class='no'>explanatory</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>.data</th>
<td><p>Data frame.</p></td>
</tr>
<tr>
<th>dependent</th>
<td><p>Character vector of length 1.</p></td>
</tr>
<tr>
<th>explanatory</th>
<td><p>Character vector of any length: name(s) of explanatory
variables.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Pass arguments <code><a href='or_plot.html'>or_plot</a></code>, <code><a href='hr_plot.html'>hr_plot</a></code>, or
<code><a href='coefficient_plot.html'>coefficient_plot</a></code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A table and a plot using <code>ggplot2</code></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Other finalfit plot functions: <code><a href='coefficient_plot.html'>coefficient_plot</a></code>,
<code><a href='hr_plot.html'>hr_plot</a></code>, <code><a href='or_plot.html'>or_plot</a></code>,
<code><a href='surv_plot.html'>surv_plot</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Coefficient plot</span>
<span class='no'>explanatory</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"age.factor"</span>, <span class='st'>"sex.factor"</span>, <span class='st'>"obstruct.factor"</span>, <span class='st'>"perfor.factor"</span>)
<span class='no'>dependent</span> <span class='kw'>=</span> <span class='st'>"nodes"</span>
<span class='no'>colon_s</span> <span class='kw'>%>%</span>
<span class='fu'>ff_plot</span>(<span class='no'>dependent</span>, <span class='no'>explanatory</span>)</div><div class='output co'>#> <span class='message'>Note: dependent includes missing data. These are dropped.</span></div><div class='output co'>#> <span class='warning'>Warning: NAs introduced by coercion</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 9 rows containing missing values (geom_point).</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 4 rows containing missing values (geom_errorbarh).</span></div><div class='img'><img src='ff_plot-1.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Odds ratio plot</span>
<span class='no'>dependent</span> <span class='kw'>=</span> <span class='st'>"mort_5yr"</span>
<span class='no'>colon_s</span> <span class='kw'>%>%</span>
<span class='fu'>ff_plot</span>(<span class='no'>dependent</span>, <span class='no'>explanatory</span>)</div><div class='output co'>#> <span class='message'>Note: dependent includes missing data. These are dropped.</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 4 rows containing missing values (geom_errorbarh).</span></div><div class='img'><img src='ff_plot-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Hazard ratio plot </span>
<span class='no'>dependent</span> <span class='kw'>=</span> <span class='st'>"Surv(time, status)"</span>
<span class='no'>colon_s</span> <span class='kw'>%>%</span>
<span class='fu'>ff_plot</span>(<span class='no'>dependent</span>, <span class='no'>explanatory</span>, <span class='kw'>dependent_label</span> <span class='kw'>=</span> <span class='st'>"Survival"</span>)</div><div class='output co'>#> <span class='message'>Dependent variable is a survival object</span></div><div class='output co'>#> <span class='warning'>Warning: Removed 4 rows containing missing values (geom_errorbarh).</span></div><div class='img'><img src='ff_plot-3.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Ewen Harrison, Tom Drake, Riinu Ots.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
</div>
</body>
</html>