automatic site/doc update [skip ci]

docs/examples/report.html

@@ -3592,7 +3592,7 @@
 <span class="navbar-brand">
   report
   <span class="navbar-author">
-    patRoon — Tue Mar 8 11:20:38 2022
+    patRoon — Tue Mar 8 12:54:12 2022
     </span>
 </span>
 

docs/handbook_bd/FCCalc.html

@@ -358,14 +358,14 @@ <h2><span class="header-section-number">8.8</span> Fold changes<a href="FCCalc.h
 #&gt; $PVTestFunc
 #&gt; function (x, y) 
 #&gt; t.test(x, y, paired = TRUE)$p.value
-#&gt; &lt;bytecode: 0x56455aa57e80&gt;
-#&gt; &lt;environment: 0x56455aa585b8&gt;
+#&gt; &lt;bytecode: 0x5563b86b7210&gt;
+#&gt; &lt;environment: 0x5563b86b7948&gt;
 #&gt; 
 #&gt; $PVAdjFunc
 #&gt; function (pv) 
 #&gt; p.adjust(pv, &quot;BH&quot;)
-#&gt; &lt;bytecode: 0x56455aa58190&gt;
-#&gt; &lt;environment: 0x56455aa585b8&gt;</code></pre>
+#&gt; &lt;bytecode: 0x5563b86b7590&gt;
+#&gt; &lt;environment: 0x5563b86b7948&gt;</code></pre>
 <p>In this example we generate a <code>list</code> with parameters in order to make a comparison between two replicate groups: <code>before</code> and <code>after</code>. Several advanced parameters are available to tweak the calculation process. These are explained in the reference manual (<code>?featureGroups</code>).</p>
 <p>The <code>as.data.table</code> function for feature groups is used to perform the FC calculations.</p>
 <div class="sourceCode" id="cb227"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb227-1"><a href="FCCalc.html#cb227-1" aria-hidden="true" tabindex="-1"></a>myFCParams <span class="ot">&lt;-</span> <span class="fu">getFCParams</span>(<span class="fu">c</span>(<span class="st">&quot;solvent-pos&quot;</span>, <span class="st">&quot;standard-pos&quot;</span>)) <span class="co"># compare solvent/standard</span></span>

docs/handbook_bd/TPs.html

@@ -339,8 +339,8 @@ <h1>
 <h1><span class="header-section-number">7</span> Transformation product screening<a href="TPs.html#TPs" class="anchor-section" aria-label="Anchor link to header"></a></h1>
 <p>This chapter describes the various functionality for screening of <em>transformation products</em> (TPs), which are introduced since <code>patRoon</code> 2.0. Screening for TPs, i.e. chemicals that are formed from a <em>parent</em> chemical by e.g. chemical or biological processes, has broad applications. For this reason, the TP screening related functionality is designed to be flexible, thus allowing one to use a workflow that is best suited for a particular study.</p>
 <p>Regardless, the TP screening workflow in <code>patRoon</code> can be roughly summarized as follows:</p>
-<div id="htmlwidget-f29571ddf96cfc0fcf4d" style="width:500px;height:90px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-f29571ddf96cfc0fcf4d">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Parent screening\" -> \"Obtaining TPs\" -> \"TP screening\" -> \"Linking parent/TPs\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-f87ac6428129b4eb810e" style="width:500px;height:90px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-f87ac6428129b4eb810e">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Parent screening\" -> \"Obtaining TPs\" -> \"TP screening\" -> \"Linking parent/TPs\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <ul>
 <li><strong>Parent screening</strong> During this step a common <code>patRoon</code> workflow is used to screen for the parent chemicals of interest. This could be a full non-target analysis with compound annotation or a relative simple suspect or target screening.</li>
 <li><strong>Obtaining TPs</strong> Data is obtained of potential TPs for the parents of interest. The TPs may originate from a library or predicted <em>in-silico</em>. Note that in some workflows this step is omitted (discussed later).</li>

docs/handbook_bd/advanced.html

@@ -365,8 +365,8 @@ <h3><span class="header-section-number">6.5.1</span> Initiating a sets workflow
 <span id="cb157-8"><a href="advanced.html#cb157-8" aria-hidden="true" tabindex="-1"></a>fGroups <span class="ot">&lt;-</span> <span class="fu">makeSet</span>(fGroupsPos, fGroupsNeg, <span class="at">groupAlgo =</span> <span class="st">&quot;openms&quot;</span>,</span>
 <span id="cb157-9"><a href="advanced.html#cb157-9" aria-hidden="true" tabindex="-1"></a>                   <span class="at">adducts =</span> <span class="fu">c</span>(<span class="st">&quot;[M+H]+&quot;</span>, <span class="st">&quot;[M-H]-&quot;</span>))</span></code></pre></div>
 <p>Visually, this workflow looks like this:</p>
-<div id="htmlwidget-aac1ce11f502e221345e" style="width:250px;height:300px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-aac1ce11f502e221345e">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = TB, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 0.6,\n         fontsize = 16,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Find features (+)\" -> \"Group features (+)\" -> \"filter (+)\" -> \"makeSet\"\n    \"Find features (-)\" -> \"Group features (-)\" -> \"filter (-)\" -> \"makeSet\"\n    \"makeSet\" -> \"...\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-9f8f31ae7c4090cd1030" style="width:250px;height:300px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-9f8f31ae7c4090cd1030">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = TB, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 0.6,\n         fontsize = 16,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Find features (+)\" -> \"Group features (+)\" -> \"filter (+)\" -> \"makeSet\"\n    \"Find features (-)\" -> \"Group features (-)\" -> \"filter (-)\" -> \"makeSet\"\n    \"makeSet\" -> \"...\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <p>Of course, any other processing steps on the feature groups data such as subsetting and <a href="intReview.html#intReview">visually checking features</a> are also possible before the sets workflow is initiated. Furthermore, it is also possible to perform <a href="incorpAdductIso.html#incorpAdductIso">adduct annotations</a> prior to grouping, which is an alternative way to improve neutralization to what <a href="setsAdducts.html#setsAdducts">was discussed before</a>.</p>
 </div>
 <div id="inspecting-and-converting-set-objects" class="section level3 hasAnchor" number="6.5.2">

docs/handbook_bd/annotation.html

@@ -338,8 +338,8 @@ <h1>
 <div id="annotation" class="section level2 hasAnchor" number="4.6">
 <h2><span class="header-section-number">4.6</span> Annotation<a href="annotation.html#annotation" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>The annotation consists of collecting MS peak lists and then formula and/or compound annotation:</p>
-<div id="htmlwidget-ecb31707b2fbb0d51795" style="width:500px;height:120px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-ecb31707b2fbb0d51795">{"x":{"diagram":"\ndigraph Annotation {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.3,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"MS peak lists\" -> \"Formula annotation\"\n    \"MS peak lists\" -> \"Compound annotation\"\n    \"Formula annotation\":n -> \"Suspect annotation\":n [style = dotted]\n    \"Compound annotation\":s -> \"Suspect annotation\":s [style = dotted]\n    \"Formula annotation\":e -> \"Compound annotation\":e [style = dotted, constraint = false]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-71776c1ad2dc8c2651d0" style="width:500px;height:120px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-71776c1ad2dc8c2651d0">{"x":{"diagram":"\ndigraph Annotation {\n  graph [ rankdir = LR ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.3,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"MS peak lists\" -> \"Formula annotation\"\n    \"MS peak lists\" -> \"Compound annotation\"\n    \"Formula annotation\":n -> \"Suspect annotation\":n [style = dotted]\n    \"Compound annotation\":s -> \"Suspect annotation\":s [style = dotted]\n    \"Formula annotation\":e -> \"Compound annotation\":e [style = dotted, constraint = false]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <p>Note that compound annotation is normally not dependent upon formula annotation. However, formula data can be used to improve ranking of candidates afterwards by the <code>addFormulaScoring()</code> function, which will be discussed later in this section. Furthermore, suspect annotation is not mandatory, and may use data from peak lists, formulae and/or comounds.</p>
 <div id="ms-peak-lists" class="section level3 hasAnchor" number="4.6.1">
 <h3><span class="header-section-number">4.6.1</span> MS peak lists<a href="annotation.html#ms-peak-lists" class="anchor-section" aria-label="Anchor link to header"></a></h3>

docs/handbook_bd/componentization.html

@@ -469,8 +469,8 @@ <h3><span class="header-section-number">4.4.1</span> Features with similar chrom
 <h3><span class="header-section-number">4.4.2</span> Homologues series<a href="componentization.html#homologues-series" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>Homologues series can be automatically detected by interfacing with the <a href="https://cran.r-project.org/web/packages/nontarget/index.html">nontarget</a> R package. Components are made from feature groups that show increasing <em>m/z</em> and retention time values. Series are first detected within each replicate group. Afterwards, series from all replicates are linked in case (partial) overlap occurs and this overlap consists of the <em>same</em> feature groups (see figure below). Linked series are then finally merged if this will not cause any conflicts with other series: such a conflict typically occurs when two series are not only linked to each other.</p>
 <div class="figure"><span style="display:block;" id="fig:HS"></span>
-<div id="htmlwidget-18feb640d28ef86d1513" style="width:600px;height:250px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-18feb640d28ef86d1513">{"x":{"diagram":"\ndigraph Homologs {\n  graph [ rankdir = LR, compound = true, style = invis ]\n  node [ shape = oval,\n         fixedsize = true,\n         width = 2.3,\n         height = 0.8,\n         fontsize = 25,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n  subgraph cluster3 {\n    I [fillcolor=skyblue]; J [fillcolor=skyblue]; K [fillcolor=skyblue]\n    G -> H -> I -> J -> K [style=invis]\n  }\n\n  subgraph cluster4 {\n    _I [label=I, fillcolor=skyblue]; X [fillcolor=indianred1]; _K [label=K, fillcolor=skyblue]\n    _I -> X -> _K -> L [style=invis]\n  }\n\n  H -> _I [ltail=cluster3, lhead=cluster4, style=invis]\n  \n  I -> _I [constraint=false, style=dashed, arrowhead=none]\n  K -> _K [constraint=false, style=dashed, arrowhead=none]\n  \n  subgraph cluster1 {\n    C [fillcolor=skyblue]; D [fillcolor=skyblue]\n    A -> B -> C -> D [style=invis]\n  }\n\n  subgraph cluster2 {\n    _C [label=C, fillcolor=skyblue]; _D [label=D, fillcolor=skyblue]\n    _C -> _D -> E -> F [style=invis]\n  }\n  \n  B -> _C [ltail=cluster1, lhead=cluster2, style=invis]\n\n  C -> _C [constraint=false, style=dashed, arrowhead=none]\n  D -> _D [constraint=false, style=dashed, arrowhead=none]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-e55413ed3c269d3d2553" style="width:600px;height:250px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-e55413ed3c269d3d2553">{"x":{"diagram":"\ndigraph Homologs {\n  graph [ rankdir = LR, compound = true, style = invis ]\n  node [ shape = oval,\n         fixedsize = true,\n         width = 2.3,\n         height = 0.8,\n         fontsize = 25,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n  subgraph cluster3 {\n    I [fillcolor=skyblue]; J [fillcolor=skyblue]; K [fillcolor=skyblue]\n    G -> H -> I -> J -> K [style=invis]\n  }\n\n  subgraph cluster4 {\n    _I [label=I, fillcolor=skyblue]; X [fillcolor=indianred1]; _K [label=K, fillcolor=skyblue]\n    _I -> X -> _K -> L [style=invis]\n  }\n\n  H -> _I [ltail=cluster3, lhead=cluster4, style=invis]\n  \n  I -> _I [constraint=false, style=dashed, arrowhead=none]\n  K -> _K [constraint=false, style=dashed, arrowhead=none]\n  \n  subgraph cluster1 {\n    C [fillcolor=skyblue]; D [fillcolor=skyblue]\n    A -> B -> C -> D [style=invis]\n  }\n\n  subgraph cluster2 {\n    _C [label=C, fillcolor=skyblue]; _D [label=D, fillcolor=skyblue]\n    _C -> _D -> E -> F [style=invis]\n  }\n  \n  B -> _C [ltail=cluster1, lhead=cluster2, style=invis]\n\n  C -> _C [constraint=false, style=dashed, arrowhead=none]\n  D -> _D [constraint=false, style=dashed, arrowhead=none]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <p class="caption">
 Figure 4.2: <strong>Linking of homologues series</strong> top: partial overlap and will be linked; bottom: no linkage due to different feature in overlapping series.
 </p>

docs/handbook_bd/features.html

@@ -338,8 +338,8 @@ <h1>
 <div id="features" class="section level2 hasAnchor" number="4.3">
 <h2><span class="header-section-number">4.3</span> Features<a href="features.html#features" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <p>Collecting features from the analyses consists of finding all features, grouping them across analyses (optionally after retention time alignment), and if desired suspect screening:</p>
-<div id="htmlwidget-8829549dd13caa367e65" style="width:500px;height:70px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-8829549dd13caa367e65">{"x":{"diagram":"\ndigraph Features {\n  graph [ rankdir = LR, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Find features\" -> \"Group features\"\n    \"Suspect screening\"\n    \"Group features\" -> \"Suspect screening\" [style=dashed]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-4bbb9234a80e865effac" style="width:500px;height:70px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-4bbb9234a80e865effac">{"x":{"diagram":"\ndigraph Features {\n  graph [ rankdir = LR, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 1,\n         fontsize = 18,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Find features\" -> \"Group features\"\n    \"Suspect screening\"\n    \"Group features\" -> \"Suspect screening\" [style=dashed]\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <div id="finding-and-grouping-features" class="section level3 hasAnchor" number="4.3.1">
 <h3><span class="header-section-number">4.3.1</span> Finding and grouping features<a href="features.html#finding-and-grouping-features" class="anchor-section" aria-label="Anchor link to header"></a></h3>
 <p>Several algorithms are available for finding features. These are listed in the table below alongside their usage and general remarks.</p>

docs/handbook_bd/initiating-a-sets-workflow.html

@@ -367,8 +367,8 @@ <h2><span class="header-section-number">6.1</span> Initiating a sets workflow<a
 <span id="cb147-14"><a href="initiating-a-sets-workflow.html#cb147-14" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb147-15"><a href="initiating-a-sets-workflow.html#cb147-15" aria-hidden="true" tabindex="-1"></a><span class="fu">reportHTML</span>(fGroups, <span class="at">MSPeakLists =</span> mslists, <span class="at">formulas =</span> formulas, <span class="at">compounds =</span> compounds)</span></code></pre></div>
 <p>This workflow will do all the steps for positive <em>and</em> negative data.</p>
-<div id="htmlwidget-f64f854b0fe189ac2ad1" style="width:250px;height:300px;" class="grViz html-widget"></div>
-<script type="application/json" data-for="htmlwidget-f64f854b0fe189ac2ad1">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = TB, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 0.6,\n         fontsize = 16,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Pre-treatment (+)\" -> \"Find features (+)\" -> \"makeSet\"\n    \"Pre-treatment (-)\" -> \"Find features (-)\" -> \"makeSet\"\n    \"makeSet\" -> \"Group features\" -> \"Annotation, ...\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-e1d9394cc3a1f1eba3c6" style="width:250px;height:300px;" class="grViz html-widget"></div>
+<script type="application/json" data-for="htmlwidget-e1d9394cc3a1f1eba3c6">{"x":{"diagram":"\ndigraph Workflow {\n  graph [ rankdir = TB, compound = true ]\n  node [ shape = box,\n         fixedsize = true,\n         width = 2.2,\n         height = 0.6,\n         fontsize = 16,\n         fillcolor = darkseagreen1,\n         style = filled ]\n\n    \"Pre-treatment (+)\" -> \"Find features (+)\" -> \"makeSet\"\n    \"Pre-treatment (-)\" -> \"Find features (-)\" -> \"makeSet\"\n    \"makeSet\" -> \"Group features\" -> \"Annotation, ...\"\n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
 <p>Only a few modifications were necessary:</p>
 <ul>
 <li>The <a href="preparations.html#anaInfo">analysis information</a> is obtained for positive and negative data (i.e. per set)</li>