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
|
<!-- 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>Plot dose-response models — drplot • drfit</title>
<!-- 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="Plot dose-response models — drplot" />
<meta property="og:description" content="Produce graphics of dose-response data and dose-response relationships
either combined or separately, for one or more substances." />
<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">drfit</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</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="../reference/index.html">Reference</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Plot dose-response models</h1>
<div class="hidden name"><code>drplot.Rd</code></div>
</div>
<div class="ref-description">
<p>Produce graphics of dose-response data and dose-response relationships
either combined or separately, for one or more substances.</p>
</div>
<pre class="usage"><span class='fu'>drplot</span>(<span class='no'>drresults</span>, <span class='no'>data</span>, <span class='no'>dtype</span>, <span class='no'>alpha</span>, <span class='no'>ctype</span>, <span class='no'>path</span>,
<span class='no'>fileprefix</span>, <span class='no'>overlay</span>, <span class='no'>xlim</span>, <span class='no'>ylim</span>, <span class='no'>xlab</span>, <span class='no'>ylab</span>, <span class='no'>axes</span>, <span class='no'>frame.plot</span>, <span class='no'>postscript</span>,
<span class='no'>pdf</span>, <span class='no'>png</span>, <span class='no'>bw</span>, <span class='no'>pointsize</span>, <span class='no'>colors</span>, <span class='no'>ltys</span>, <span class='no'>pchs</span>, <span class='no'>devoff</span>, <span class='no'>lpos</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>drresults</th>
<td><p>A data frame as returned from <code><a href='drfit.html'>drfit</a></code>.</p></td>
</tr>
<tr>
<th>data</th>
<td><p>A data frame as returned from <code><a href='drdata.html'>drdata</a></code>. The data frame has to
contain at least a factor called "substance", a vector called "unit"
containing the unit used for the dose, a column "response" with the
response values of the test system normalized between 0 and 1, a column
"dose" with the numeric dose values and a factor called "dosefactor"
containing the dose as a factor.</p></td>
</tr>
<tr>
<th>dtype</th>
<td><p>A string describing if the raw data should be plotted ("raw"), or an error
bar should be constructed from the standard deviations of the responses at
each dose level ("std", default value) or from the confidence intervals
("conf"). If you don't want to see the data, set it to "none".</p></td>
</tr>
<tr>
<th>alpha</th>
<td><p>The confidence level, defaulting to 0.95, only used if dtype "conf" has been
chosen.</p></td>
</tr>
<tr>
<th>ctype</th>
<td><p>This argument decides if horizontal lines are drawn to show the scatter of
the control values (dose = 0), if there are more than three of them.
Defaults to "none", further allowed values are "std" and "conf" for
displaying the standard deviation of the controls or the confidence
interval for the mean of the controls.</p></td>
</tr>
<tr>
<th>path</th>
<td><p>The path where graphic files should be put if any are produced. Defaults
to "./" i.e. the current working directory of R.</p></td>
</tr>
<tr>
<th>fileprefix</th>
<td><p>A string which will form the beginning of each filename, if graphic files
are created. Defaults to "drplot".</p></td>
</tr>
<tr>
<th>overlay</th>
<td><p>If TRUE, all output will be put into one graph, otherwise a separate graph
will be created for each substance.</p></td>
</tr>
<tr>
<th>xlim</th>
<td><p>The plot limits (min,max) on the dose axis.</p></td>
</tr>
<tr>
<th>ylim</th>
<td><p>The plot limits (min,max) on the response axis.</p></td>
</tr>
<tr>
<th>xlab</th>
<td><p>The axis title for the x axis. Defaults to "Concentration in" <code>unit</code>.</p></td>
</tr>
<tr>
<th>ylab</th>
<td><p>The axis title for the y axis. Defaults to "Normalized response".</p></td>
</tr>
<tr>
<th>axes</th>
<td><p>Specifies if axes should be drawn. Default is TRUE, as in
<code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td>
</tr>
<tr>
<th>frame.plot</th>
<td><p>Specifies if the plot should be framed. Default is TRUE, as in
<code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td>
</tr>
<tr>
<th>postscript</th>
<td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if
the pdf and png arguments are also FALSE, graphics will be
displayed with a screen graphics device.</p></td>
</tr>
<tr>
<th>pdf</th>
<td><p>If TRUE, (a) pdf graph(s) will be created. Otherwise, and if
the postscript, and png arguments are also FALSE, graphics will be
displayed with a screen graphics device.</p></td>
</tr>
<tr>
<th>png</th>
<td><p>If TRUE, (a) png graph(s) will be created. Otherwise, and if the
postscript and pdf arguments are also FALSE, graphics will be displayed
with a screen graphics device.</p></td>
</tr>
<tr>
<th>bw</th>
<td><p>A boolean deciding if the plots will be black and white or not. Default
is TRUE.</p></td>
</tr>
<tr>
<th>pointsize</th>
<td><p>The pointsize used for pdf, png and postscript graphics.</p></td>
</tr>
<tr>
<th>colors</th>
<td><p>This is a vector of colors, defaulting to 1:8, used for plotting the data.</p></td>
</tr>
<tr>
<th>ltys</th>
<td><p>This is a vector of line types for the dose-response models, defaulting to 1:8.</p></td>
</tr>
<tr>
<th>pchs</th>
<td><p>This is a vector of character types for the data. The default uses built-in
characters 1:n with n being the number of substances for which data are plotted
for overlays, or always 1 when no overlay plot is generated.</p></td>
</tr>
<tr>
<th>lpos</th>
<td><p>An optional argument defaulting to "topright" specifying the position
of the legend by being passed to the legend function. See the help for the
legend function for all possiblities.</p></td>
</tr>
<tr>
<th>devoff</th>
<td><p>If set to FALSE, the device will not be closed after creation of an overlay
pdf, png or postscript graph, so texts and other elements can
be added.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p></p>
<dt>results</dt><dd><p>You will get plots of data and/or the fitted dose-response curves, on the
screen and/or as postscript/pdf/png files, depending on the parameters.</p></dd>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>There is a demo for each dataset that can be accessed by
<code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>)
<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>)</div><div class='img'><img src='drplot-1.png' alt='' width='700' height='433' /></div><div class='img'><img src='drplot-2.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="#note">Note</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<h2>Author</h2>
<p>Johannes Ranke
<a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</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>
|
