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within the simplerspec framework. Returns plots based on ggplot2
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(class "ggplot"). Different spectra types such as raw or preprocessed spectra
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and groups can be differentiated by different colors or by using panels
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(so called facets). Additionally, spectra can be colored based on an
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additional measure variable, e.g. determined by chemical reference analysis.'><!-- 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]>
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<h1>ggplot2 wrapper for extended spectra plotting</h1>
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<small class="dont-index">Source: <a href="https://github.com/philipp-baumann/simplerspec/blob/HEAD/R/plot-spc-extended.R" class="external-link"><code>R/plot-spc-extended.R</code></a></small>
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<div class="hidden name"><code>plot_spc_ext.Rd</code></div>
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</div>
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<div class="ref-description">
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<p><code>plot_spc_ext</code> is a custom plotting function developed
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within the simplerspec framework. Returns plots based on ggplot2
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(class "ggplot"). Different spectra types such as raw or preprocessed spectra
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and groups can be differentiated by different colors or by using panels
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(so called facets). Additionally, spectra can be colored based on an
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additional measure variable, e.g. determined by chemical reference analysis.</p>
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</div>
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<div id="ref-usage">
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">plot_spc_ext</span><span class="op">(</span></span>
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<span> <span class="va">spc_tbl</span>,</span>
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<span> spc_tbl_l <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> lcols_spc <span class="op">=</span> <span class="st">"spc"</span>,</span>
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<span> lcol_measure <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> lcol_measure_col_palette <span class="op">=</span> <span class="st">"Spectral"</span>,</span>
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<span> lcol_measure_col_direction <span class="op">=</span> <span class="op">-</span><span class="fl">1</span>,</span>
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<span> spc_id <span class="op">=</span> <span class="st">"unique_id"</span>,</span>
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<span> group_id <span class="op">=</span> <span class="st">"sample_id"</span>,</span>
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<span> group_id_order <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> group_color <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> group_color_palette <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> group_panel <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> group_legend <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> ncol <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> relabel_spc <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> ylab <span class="op">=</span> <span class="st">"Spectrum value"</span>,</span>
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<span> alpha <span class="op">=</span> <span class="fl">0.5</span>,</span>
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<span> line_width <span class="op">=</span> <span class="fl">0.2</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>spc_tbl</dt>
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<dd><p>Tibble data frame containing spectra, x-axis values, metadata
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and eventual measured variables as list-columns.</p></dd>
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<dt>spc_tbl_l</dt>
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<dd><p>List of spectral tibbles (data frames). Default is
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<code>NULL</code> (argument is not used).</p></dd>
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<dt>lcols_spc</dt>
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<dd><p>Character vector of spectral list-columns to be extracted.
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Default is <code>"spc"</code> (raw spectra).</p></dd>
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<dt>lcol_measure</dt>
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<dd><p>Character vector of length 1 denoting the column name
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of the measure columns. This argument is optional. Default is <code>NULL</code>,
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which does not extract an additional measure column.</p></dd>
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<dt>lcol_measure_col_palette</dt>
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<dd><p>Palette value supplied to
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<code>ggplot::scale_colour_brewer()</code>. Default is <code>"Spectral"</code>, but you can set
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it to the default argument <code>1</code> (will use
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<code>scale_colour_brewer(..., palette = 1)</code>).</p></dd>
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<dt>lcol_measure_col_direction</dt>
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<dd><p>Sets the the order of colours in the scale
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that is based on a measure column. Default is <code>-1</code> which reverses the
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scale. Argument is passed on to the function <code>ggplot2::sclae_colour_brewer()</code>
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as argument <code>direction</code>.</p></dd>
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<dt>spc_id</dt>
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<dd><p>Character vector denoting column name for a unique spectrum ID.
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Default is <code>"unique_id"</code>.</p></dd>
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<dt>group_id</dt>
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<dd><p>Character vector denoting column name for the spectrum group
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ID. Default is <code>"sample_id"</code>. The group ID is used for
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plotting spectra by group (e.g. by using different colors or panels).</p></dd>
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<dt>group_id_order</dt>
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<dd><p>Logical that specifies whether the panel names
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derived from a numeric <code>group_id</code> column are reordered using ascending
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numbers. Default is <code>TRUE</code>.</p></dd>
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<dt>group_color</dt>
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<dd><p>Logical defining whether spectra are colored by the column
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specified by <code>group_id</code>.</p></dd>
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<dt>group_color_palette</dt>
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<dd><p>Character (1L) defining the diverging colour
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scales from colorbrewer.org; see <code>?scale_colour_brewer</code> for supported
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diverging colur types (<code>palette</code> argument).</p></dd>
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<dt>group_panel</dt>
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<dd><p>Logical defining whether spectra are arranged into panels
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by groups specified in <code>group_id</code>. Default is <code>TRUE</code>.</p></dd>
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<dt>group_legend</dt>
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<dd><p>Logical defining whether a legend for the <code>group_id</code>
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is plotted. Default is <code>FALSE</code>.</p></dd>
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<dt>ncol</dt>
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<dd><p>Integer vector of length 1. Defines number of columns when
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plotting panels (facets). Default is <code>NULL</code> (argument not used).</p></dd>
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<dt>relabel_spc</dt>
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<dd><p>Logical defining whether panels are relabeled with custom
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names for spectra types. Default is TRUE. When <code>TRUE</code>, arguments
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from <code>relabel_spc_types</code> can be passed to <code>plot_spc_ext</code>
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(supported via the <code>...</code> (ellipsis) argument)</p></dd>
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<dt>ylab</dt>
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<dd><p>Character vector or vector of type <code>"expression"</code> created by
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mathematical expression created by <code>expression</code>. Custom annotation for
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y-axis of spectra</p></dd>
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<dt>alpha</dt>
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<dd><p>Integer of length 1, from 0 to 1. Defines transparency of
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spectral lines. Default is <code>0.5</code> (0 is completely transparent and
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1 is no transparency).</p></dd>
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<dt>line_width</dt>
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<dd><p>Numeric vector of length 1 specifying the width of the
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spectral lines. Default is <code>0.2</code>.</p></dd>
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<dt>...</dt>
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<dd><p>Further arguments to be passed to <code>plot_spc_ext</code>. Currently,
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arguments of <code>relabel_spc_types</code> are supported.</p></dd>
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</dl></div>
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<div id="value">
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<h2>Value</h2>
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<p>Object of class <code>"ggplot"</code> (ggplot2 graph).</p>
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</div>
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<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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<p></p><p>Developed by Philipp Baumann.</p>
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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