diff --git a/docs/404.html b/docs/404.html
index c80986ed68c58517ff2360490fa03ad5da3aebff..3bcab9a088d984ab7152ab084a66c9c715dd82ad 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index fa1d6428a143ef9265c0711cd4b3454099ec49ef..2986e697537c20ddfeb1967e46abf91ff135d4fc 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/index.html b/docs/index.html
index 15ad32aef4f4b21ff80845775b49634f0cf231f3..3caddf948aede3d844a26196a8238cfe20cd02e8 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -67,7 +67,7 @@
 <div id="cluster-lookup-tables---cluster-luts" class="section level1">
 <div class="page-header"><h1 class="hasAnchor">
 <a href="#cluster-lookup-tables---cluster-luts" class="anchor"></a>Cluster Lookup Tables - cluster LUTs</h1></div>
-<p>Coloring for a cluster tree with 145 leaves and 28 levels (10 (top), 15, …, 145 clusters (bottom)): <img src="docs/reference/colortree.png" alt="colortree"></p>
+<p>Coloring for a cluster tree with 145 leaves and 28 levels (10 (top), 15, …, 145 clusters (bottom)): <img src="reference/colortree.png" alt="colortree"></p>
 <div id="concepts" class="section level2">
 <h2 class="hasAnchor">
 <a href="#concepts" class="anchor"></a>Concepts</h2>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 691938f0e41b1006c60f6669c01e3c4b715d7c96..49c646adbe362f686345fa0941ee47e8914566ba 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.7.3
 pkgdown: 1.5.1
 pkgdown_sha: ~
 articles: []
-last_built: 2020-08-03T09:48Z
+last_built: 2020-08-06T02:10Z
 
diff --git a/docs/reference/ColorShadeRamp.html b/docs/reference/ColorShadeRamp.html
index e8683b3124cbb8248ca62ef9437a6e46d1e55128..82103f37936deddaa1fcbc1ed9010abc38c5d916 100644
--- a/docs/reference/ColorShadeRamp.html
+++ b/docs/reference/ColorShadeRamp.html
@@ -73,7 +73,7 @@ for symmetry the color should be a color with full saturation" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/between.html b/docs/reference/between.html
index 25fbfc26fd6bfc8a903185ff52201fcc48d43126..08d0d31c75dd60c5ce13d724ea090b14e5ebde1a 100644
--- a/docs/reference/between.html
+++ b/docs/reference/between.html
@@ -73,7 +73,7 @@ margins), i.e., \(low \leq x \leq high\)" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/col.rep.html b/docs/reference/col.rep.html
index 4134eed37e33ca008cd1822f1aff800c09a9da18..f785628daac36660c37c69cf0786678de7df245d 100644
--- a/docs/reference/col.rep.html
+++ b/docs/reference/col.rep.html
@@ -73,7 +73,7 @@ RGB color matrix. Analog to rep which is used internally." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -114,7 +114,7 @@ RGB color matrix. Analog to rep which is used internally." />
 RGB color matrix. Analog to <code><a href='https://rdrr.io/r/base/rep.html'>rep</a></code> which is used internally.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>col.rep</span>(<span class='no'>col</span>, <span class='no'>n</span>)</pre>
+    <pre class="usage"><span class='fu'>col.rep</span>(<span class='no'>col</span>, <span class='no'>n</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -127,11 +127,22 @@ RGB color matrix. Analog to <code><a href='https://rdrr.io/r/base/rep.html'>rep<
       <th>n</th>
       <td><p>number of repetitions (should be a positive integer value)</p></td>
     </tr>
+    <tr>
+      <th>alpha</th>
+      <td><p>either logical or actual alpha (in [0..255])</p></td>
+    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>color matrix with <code>n</code> columns of color <code>col</code></p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>If <code>col</code> consists of more than one color, those colors are recycl
+the usual rules to reach <code>n</code> colors. In the special case where <code>n</code>
+is smaller than thenumber of colors in <code>col</code>, only the first <code>n</code>
+colors will be returned.</p>
+<p>For <code>n</code>&lt;1 an empty matrix is returned.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='fu'>col.rep</span>(<span class='st'>'red'</span>, <span class='fl'>3</span>)</div><div class='output co'>#&gt;      [,1] [,2] [,3]
diff --git a/docs/reference/colmat2lutfile.html b/docs/reference/colmat2lutfile.html
new file mode 100644
index 0000000000000000000000000000000000000000..5c60840f7a70b287cf14dfde5b93338467e15dcd
--- /dev/null
+++ b/docs/reference/colmat2lutfile.html
@@ -0,0 +1,193 @@
+<!-- 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>Write color matrix to LUT file — colmat2lutfile • clusterLUTs</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="Write color matrix to LUT file — colmat2lutfile" />
+<meta property="og:description" content="Companion function to writelut that sets up a correct
+lookup table." />
+
+
+
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <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">clusterLUTs</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</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>Write color matrix to LUT file</h1>
+    
+    <div class="hidden name"><code>colmat2lutfile.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Companion function to <code><a href='writelut.html'>writelut</a></code> that sets up a correct
+lookup table.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>colmat2lutfile</span>(
+  <span class='no'>colmat</span>,
+  <span class='no'>file</span>,
+  <span class='kw'>fill</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>length</span> <span class='kw'>=</span> <span class='fl'>256</span>,
+  <span class='kw'>bw</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>truncate</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>colmat</th>
+      <td><p>color matrix</p></td>
+    </tr>
+    <tr>
+      <th>file</th>
+      <td><p>file to write to</p></td>
+    </tr>
+    <tr>
+      <th>fill</th>
+      <td><p>whether to fill</p></td>
+    </tr>
+    <tr>
+      <th>length</th>
+      <td><p>desired length (only when <code>fill</code> is TRUE)</p></td>
+    </tr>
+    <tr>
+      <th>bw</th>
+      <td><p>add 'black' as first and 'white' as last entry?</p></td>
+    </tr>
+    <tr>
+      <th>truncate</th>
+      <td><p>truncate if too long</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>ignored</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>color matrix that was written (possibly filled)</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>colmat2lutfile</span>(<span class='fu'><a href='rainbow_lab.html'>rainbow_lab</a></span>(<span class='fl'>6</span>), <span class='fu'><a href='https://rdrr.io/r/base/tempfile.html'>tempfile</a></span>(), <span class='kw'>fill</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Benno Pütz.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/reference/color.shades.html b/docs/reference/color.shades.html
index 9b4e41a63ae861a6787274400a8c47d397c19b1d..d3e6173029b5a3a6ece0e3a43ab6924d10481109 100644
--- a/docs/reference/color.shades.html
+++ b/docs/reference/color.shades.html
@@ -74,7 +74,7 @@ shades are going scale of the way to white/black." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/concat.tbl.list.html b/docs/reference/concat.tbl.list.html
index f1a9e8d4cb770bfe982c503b5dbc8c4ad8c6b899..6bf0c9fa7ddc6cf56c474a7e7873def1d007c505 100644
--- a/docs/reference/concat.tbl.list.html
+++ b/docs/reference/concat.tbl.list.html
@@ -76,7 +76,7 @@ via cbind." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/cutshades.html b/docs/reference/cutshades.html
index fc50903c91e2ec8a153bbc8feac1f8a70661c828..fbea5ee579ec8dc0b2a37450e31e91d8c55f02d0 100644
--- a/docs/reference/cutshades.html
+++ b/docs/reference/cutshades.html
@@ -74,7 +74,7 @@ reorder the shading to arrange according to cluster members." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/default.cuts.html b/docs/reference/default.cuts.html
new file mode 100644
index 0000000000000000000000000000000000000000..63ef72235fe8f5a34a391e47ae5568d668c88fa1
--- /dev/null
+++ b/docs/reference/default.cuts.html
@@ -0,0 +1,168 @@
+<!-- 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>default cuts — default.cuts • clusterLUTs</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="default cuts — default.cuts" />
+<meta property="og:description" content="find suitable cuts for n leaves" />
+
+
+
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <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">clusterLUTs</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</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>default cuts</h1>
+    
+    <div class="hidden name"><code>default.cuts.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>find suitable cuts for <code>n</code> leaves</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>default.cuts</span>(<span class='no'>n</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>n</th>
+      <td><p>number of leaves in dendrogram</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>ignored</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>nice cuts</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>Internal</p>
+<p>For a square <code>n</code> the cuts are the multiples of \(\sqrt{n}\)
+up to  {n</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>default.cuts</span>(<span class='fl'>9</span>)</div><div class='output co'>#&gt; <span class='error'>Error in default.cuts(9): could not find function "default.cuts"</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Benno Pütz.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/reference/default.hcl.html b/docs/reference/default.hcl.html
index 28534f422499f2acf9f366f37e4ec64fd8d4f564..720566818e42c8c35ce2c0fe9f584d3bf1376edc 100644
--- a/docs/reference/default.hcl.html
+++ b/docs/reference/default.hcl.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/default.lab.html b/docs/reference/default.lab.html
index 5cad0aaad2ff2a5afe05e513f67f3efbc2bb3168..cb268aadc31b7cb54d356cd7bd2e713d172a53e7 100644
--- a/docs/reference/default.lab.html
+++ b/docs/reference/default.lab.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/default.rgb.html b/docs/reference/default.rgb.html
index 149eec11ea17293fc82b766a2c39a99ce9fdd39e..ece7b2c63d616f9691d3b3d222c1213a12492722 100644
--- a/docs/reference/default.rgb.html
+++ b/docs/reference/default.rgb.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/dend.with.cuts.html b/docs/reference/dend.with.cuts.html
index b38d3c721ff223eb9c24b760fb82bc6a4eda0eb9..930cd6a150712e313d11702b5a118eb4e37ffb1b 100644
--- a/docs/reference/dend.with.cuts.html
+++ b/docs/reference/dend.with.cuts.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -112,15 +112,11 @@
     <p>Mainly for debugging</p>
     </div>
 
-    <pre class="usage"><span class='fu'>dend.with.cuts</span>(<span class='no'>dt</span>, <span class='kw'>cuts</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>cut.col</span> <span class='kw'>=</span> <span class='st'>"#ffa050"</span>, <span class='no'>...</span>)</pre>
+    <pre class="usage"><span class='fu'>dend.with.cuts</span>(<span class='no'>hc.or.dt</span>, <span class='kw'>cuts</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>cut.col</span> <span class='kw'>=</span> <span class='st'>"#ffa050"</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>dt</th>
-      <td><p>output of <code><a href='dummy.tree.html'>dummy.tree</a></code></p></td>
-    </tr>
     <tr>
       <th>cuts</th>
       <td><p>cut levels to show (cluster numbers) (optional, see description)</p></td>
@@ -133,6 +129,10 @@
       <th>...</th>
       <td><p>passed to <code><a href='https://rdrr.io/r/graphics/abline.html'>abline</a></code> (<code>col</code>, <code>lty</code>, ...)</p></td>
     </tr>
+    <tr>
+      <th>dt</th>
+      <td><p>output of <code><a href='dummy.tree.html'>dummy.tree</a></code></p></td>
+    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
diff --git a/docs/reference/dummy.tree.html b/docs/reference/dummy.tree.html
index 795ca05b1e22bcf2de35cfc555d7f13faec47101..596b400753d0f32cb2e839cce6ad3ca31708eb55 100644
--- a/docs/reference/dummy.tree.html
+++ b/docs/reference/dummy.tree.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -112,12 +112,7 @@
     <p>The number shoud be reasonably small to keep the example results clear.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>dummy.tree</span>(
-  <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>9</span>,
-  <span class='kw'>cuts</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>n</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span>(<span class='no'>n</span> + <span class='fl'>1</span>)))[-<span class='fl'>1</span>]),
-  <span class='no'>...</span>,
-  <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>1234</span>
-)</pre>
+    <pre class="usage"><span class='fu'>dummy.tree</span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>9</span>, <span class='kw'>cuts</span> <span class='kw'>=</span> <span class='fu'><a href='default.cuts.html'>default.cuts</a></span>(<span class='no'>n</span>), <span class='no'>...</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>1234</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
diff --git a/docs/reference/expand.colmat.html b/docs/reference/expand.colmat.html
new file mode 100644
index 0000000000000000000000000000000000000000..3de96fccec617da10ee9cae103007eddae554027
--- /dev/null
+++ b/docs/reference/expand.colmat.html
@@ -0,0 +1,175 @@
+<!-- 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>expand color matrix — expand.colmat • clusterLUTs</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="expand color matrix — expand.colmat" />
+<meta property="og:description" content="Add entries with fill.col to reach length colors in
+color matrix." />
+
+
+
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <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">clusterLUTs</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</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>expand color matrix</h1>
+    
+    <div class="hidden name"><code>expand.colmat.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Add entries with <code>fill.col</code> to reach <code>length</code> colors in
+color matrix.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>expand.colmat</span>(<span class='no'>cm</span>, <span class='kw'>length</span> <span class='kw'>=</span> <span class='fl'>256</span>, <span class='kw'>fill.col</span> <span class='kw'>=</span> <span class='st'>"#000000"</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>cm</th>
+      <td><p>color matrix (or valid input to <code><a href='https://rdrr.io/r/grDevices/col2rgb.html'>col2rgb</a></code>)</p></td>
+    </tr>
+    <tr>
+      <th>length</th>
+      <td><p>desired number of color entries</p></td>
+    </tr>
+    <tr>
+      <th>fill.col</th>
+      <td><p>color to fill matrix with ('black')</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>ignored</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>expanded color matrix</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>Should <code>cm</code> have more entries than specified by <code>length</code>,
+the input martix is returned unchanged</p>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Benno Pütz.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/reference/grapes-and-grapes.html b/docs/reference/grapes-and-grapes.html
index 9ad25ffd124ff5f614409ace97646303ecb76726..f5f8a5fec02aae1cc7e41dfb67f4da22a5b4c5fb 100644
--- a/docs/reference/grapes-and-grapes.html
+++ b/docs/reference/grapes-and-grapes.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/hri.plot-1.png b/docs/reference/hri.plot-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..dcd1fc1da95f324fe522571fbc059fe4f09bb709
Binary files /dev/null and b/docs/reference/hri.plot-1.png differ
diff --git a/docs/reference/hri.plot-2.png b/docs/reference/hri.plot-2.png
new file mode 100644
index 0000000000000000000000000000000000000000..b897ac96ca9a88c1c774646345a8bb35c5c3b85a
Binary files /dev/null and b/docs/reference/hri.plot-2.png differ
diff --git a/docs/reference/hri.plot.html b/docs/reference/hri.plot.html
new file mode 100644
index 0000000000000000000000000000000000000000..1562140c1ebbe5fcbc8308f48422d14a1b1cdcac
--- /dev/null
+++ b/docs/reference/hri.plot.html
@@ -0,0 +1,183 @@
+<!-- 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>hue range init plot — hri.plot • clusterLUTs</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="hue range init plot — hri.plot" />
+<meta property="og:description" content="for internal testing" />
+
+
+
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <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">clusterLUTs</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</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>hue range init plot</h1>
+    
+    <div class="hidden name"><code>hri.plot.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>for internal testing</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>hri.plot</span>(<span class='no'>hues</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>yoff</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</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>hues</th>
+      <td><p>hue seeds, passed to <code><a href='hue.range.init.html'>hue.range.init</a></code></p></td>
+    </tr>
+    <tr>
+      <th>y</th>
+      <td><p>y-level to show hue range line on (0..1)</p></td>
+    </tr>
+    <tr>
+      <th>yoff</th>
+      <td><p>y-offset for start/end markers</p></td>
+    </tr>
+    <tr>
+      <th>add</th>
+      <td><p>add to existing plot?</p></td>
+    </tr>
+    <tr>
+      <th>limits</th>
+      <td><p>passed to  <code><a href='hue.range.init.html'>hue.range.init</a></code></p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>passed to <code><a href='hue.range.init.html'>hue.range.init</a></code> (<code>limits</code>, <code>symmetric</code>)</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>new hue range (invisibly)</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>Show hue ranges created by <code><a href='hue.range.init.html'>hue.range.init</a></code>.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='kw pkg'>clusterLUTs</span><span class='kw ns'>:::</span><span class='fu'>hri.plot</span>(<span class='fl'>1</span>:<span class='fl'>5</span>/<span class='fl'>6</span>)</div><div class='img'><img src='hri.plot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='no'>hues</span>  <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.2</span>, <span class='fl'>.4</span>, <span class='fl'>.7</span>, <span class='fl'>5</span>/<span class='fl'>6</span>)
+<span class='kw pkg'>clusterLUTs</span><span class='kw ns'>:::</span><span class='fu'>hri.plot</span>(<span class='no'>hues</span>,                                  <span class='kw'>yo</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</div><div class='input'><span class='kw pkg'>clusterLUTs</span><span class='kw ns'>:::</span><span class='fu'>hri.plot</span>(<span class='no'>hues</span>,                     <span class='kw'>symm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>yo</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='input'><span class='kw pkg'>clusterLUTs</span><span class='kw ns'>:::</span><span class='fu'>hri.plot</span>(<span class='no'>hues</span>, <span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.3</span>, <span class='fl'>.8</span>),              <span class='kw'>yo</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='input'><span class='kw pkg'>clusterLUTs</span><span class='kw ns'>:::</span><span class='fu'>hri.plot</span>(<span class='no'>hues</span>, <span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.3</span>, <span class='fl'>.8</span>), <span class='kw'>symm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>yo</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='hri.plot-2.png' alt='' width='700' height='433' /></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Benno Pütz.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/reference/hue.range.colors.html b/docs/reference/hue.range.colors.html
index fac081068ffd4b9193b957580edcea43f2313f81..f984428460fedfa8fa2366a83e864daab604e21a 100644
--- a/docs/reference/hue.range.colors.html
+++ b/docs/reference/hue.range.colors.html
@@ -74,7 +74,7 @@ the whole matrix is divided by 255." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/hue.range.init.html b/docs/reference/hue.range.init.html
new file mode 100644
index 0000000000000000000000000000000000000000..bdd115857c378bb39a3e4581a57e3c4d82e11609
--- /dev/null
+++ b/docs/reference/hue.range.init.html
@@ -0,0 +1,184 @@
+<!-- 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>hue range initialization — hue.range.init • clusterLUTs</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="hue range initialization — hue.range.init" />
+<meta property="og:description" content="Initialize a hue range &quot;seeded&quot; by hues. It is attempted to
+allocate the range given by limits sparing a fraction of
+blank for the breaks. If symmetric is set, the hue
+ranges are centered around the seed values (except when at the
+limits) leaving more of the hue space unallocated." />
+
+
+
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <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">clusterLUTs</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</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>hue range initialization</h1>
+    
+    <div class="hidden name"><code>hue.range.init.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Initialize a hue range "seeded" by <code>hues</code>. It is attempted to
+allocate the range given by <code>limits</code> sparing a fraction of
+<code>blank</code> for the breaks. If <code>symmetric</code> is set, the hue
+ranges are centered around the seed values (except when at the
+limits) leaving more of the hue space unallocated.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>hue.range.init</span>(<span class='kw'>hues</span> <span class='kw'>=</span> <span class='fl'>5</span>/<span class='fl'>12</span>, <span class='kw'>blank</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>symmetric</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>hues</th>
+      <td><p>initial "centers"</p></td>
+    </tr>
+    <tr>
+      <th>blank</th>
+      <td><p>fraction of full range (given by <code>limits</code>) not to assign</p></td>
+    </tr>
+    <tr>
+      <th>limits</th>
+      <td><p>define full range of available hues</p></td>
+    </tr>
+    <tr>
+      <th>symmetric</th>
+      <td><p>range symmetric around <code>hues</code> (where possible)</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>ignored</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>new hue range</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>The values in <code>hues</code> are trimmed to [0..1] and duplicates are removed.</p>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Benno Pütz.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/reference/hue.range.lines.html b/docs/reference/hue.range.lines.html
index 14bf7055ed73eec96d3ad548e6efe7758f77f925..bdc79b183944aa5d73b197f5f704839bda3d72f8 100644
--- a/docs/reference/hue.range.lines.html
+++ b/docs/reference/hue.range.lines.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/hue.range.split.html b/docs/reference/hue.range.split.html
index 77077bf005423904cb5bd5525f12c0ffbbfb71f2..e87e50ee8cf9ffca9dfd576ef6b3e46108bc2573 100644
--- a/docs/reference/hue.range.split.html
+++ b/docs/reference/hue.range.split.html
@@ -73,7 +73,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -114,7 +114,7 @@
 2-element vector or a \(2xN\) matrix where each column defines such a range.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>hue.range.split</span>(<span class='no'>hue.range</span>, <span class='no'>split.tbl</span>, <span class='kw'>blank</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
+    <pre class="usage"><span class='fu'>hue.range.split</span>(<span class='no'>hue.range</span>, <span class='no'>split.tbl</span>, <span class='kw'>blank</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='no'>...</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -133,6 +133,10 @@ vectors applied to corresponding matrix colunm)</p></td>
       <th>blank</th>
       <td><p>which fraction of the range should be left blank</p></td>
     </tr>
+    <tr>
+      <th>...</th>
+      <td><p>ignored</p></td>
+    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 64e38c275e3a381a3ebc1c996a2848cda3a1b8c6..6f435694ba80e10c9864c3dc20280fdd70179bdc 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -145,6 +145,12 @@
         <td><p>color repetition</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="colmat2lutfile.html">colmat2lutfile()</a></code> </p>
+        </td>
+        <td><p>Write color matrix to LUT file</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="color.shades.html">color.shades()</a></code> </p>
         </td>
@@ -163,6 +169,12 @@
         <td><p>prepare shades and reorder to match cut</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="default.cuts.html">default.cuts()</a></code> </p>
+        </td>
+        <td><p>default cuts</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="default.hcl.html">default.hcl()</a></code> </p>
         </td>
@@ -193,18 +205,36 @@
         <td><p>dummy tree data for examples</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="expand.colmat.html">expand.colmat()</a></code> </p>
+        </td>
+        <td><p>expand color matrix</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="grapes-and-grapes.html">`%&amp;%`</a></code> </p>
         </td>
         <td><p>binary bitwise AND</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="hri.plot.html">hri.plot()</a></code> </p>
+        </td>
+        <td><p>hue range init plot</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="hue.range.colors.html">hue.range.colors()</a></code> </p>
         </td>
         <td><p>convert hue range matrix to corresponding colors</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="hue.range.init.html">hue.range.init()</a></code> </p>
+        </td>
+        <td><p>hue range initialization</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="hue.range.lines.html">hue.range.lines()</a></code> </p>
         </td>
@@ -313,6 +343,12 @@
         <td><p>show sub tables</p></td>
       </tr><tr>
         
+        <td>
+          <p><code><a href="subtables.html">subtables()</a></code> </p>
+        </td>
+        <td><p>subtables</p></td>
+      </tr><tr>
+        
         <td>
           <p><code><a href="tbl2mat.html">tbl2mat()</a></code> </p>
         </td>
diff --git a/docs/reference/init.blank.plot.html b/docs/reference/init.blank.plot.html
index d42e3bce126a652520233bf88708a23c0c52868c..6ca3b502e4cfaa1e07076622843705697ed6ba55 100644
--- a/docs/reference/init.blank.plot.html
+++ b/docs/reference/init.blank.plot.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/init.huerange.plot.html b/docs/reference/init.huerange.plot.html
index 3e87ca48509e3380dc6e200b4635934a481850a4..b5cabd1a976c6b06d5fb67860b241a9e5eac445b 100644
--- a/docs/reference/init.huerange.plot.html
+++ b/docs/reference/init.huerange.plot.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/mat2list.html b/docs/reference/mat2list.html
index f8068208619b2f01ae26a86b71093dcc1f314534..6dcfae1896fdaa3376e9ac0ae92f8274eebbef8b 100644
--- a/docs/reference/mat2list.html
+++ b/docs/reference/mat2list.html
@@ -73,7 +73,7 @@ or row vectors  (which == 1)." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/rainbow_lab.html b/docs/reference/rainbow_lab.html
index 4b718a25a35aae80ed6f6e76628046024437094f..12a9c4a06910259f7e2c8ef115e4d48fbcb30747 100644
--- a/docs/reference/rainbow_lab.html
+++ b/docs/reference/rainbow_lab.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/rainbow_lab_ramp.html b/docs/reference/rainbow_lab_ramp.html
index f7057b2276722cf2b852f130f8376eb80fe46388..a8383c6d25c896b3076e094a65e8e31260152594 100644
--- a/docs/reference/rainbow_lab_ramp.html
+++ b/docs/reference/rainbow_lab_ramp.html
@@ -73,7 +73,7 @@ between neighboring colors." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/randomize.cutree.html b/docs/reference/randomize.cutree.html
index edb603af9af976b4547b80a7f6336a676c7e3c68..3b4a986f29692031952a101f7c67e9f6ce5c4a2b 100644
--- a/docs/reference/randomize.cutree.html
+++ b/docs/reference/randomize.cutree.html
@@ -75,7 +75,7 @@ Matlab counterpart (or what read.tree produces of it)." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/read.tree.html b/docs/reference/read.tree.html
index 81885192eecae82ecd6592da36e0d134ef962bbc..5cf4940514ae8ced468b181eeaf8e3b8da7952a9 100644
--- a/docs/reference/read.tree.html
+++ b/docs/reference/read.tree.html
@@ -75,7 +75,7 @@ entries)" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/readlut.html b/docs/reference/readlut.html
index 43b6dd8b12545ced9c968165d0e3a159cf02c905..e22c262c3ed8a2d26a6f3604864abff987617689 100644
--- a/docs/reference/readlut.html
+++ b/docs/reference/readlut.html
@@ -73,7 +73,7 @@ return a color matrix with columns corresponding to the color entries (RGB)." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/reidx.cut.html b/docs/reference/reidx.cut.html
index 147cde7ebb843c290eed386227bd9e46819a382c..2be6ae7df2188f9bddfcb3ed1338f3c87a51fcaf 100644
--- a/docs/reference/reidx.cut.html
+++ b/docs/reference/reidx.cut.html
@@ -73,7 +73,7 @@ can be preserved" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/show.brain.lut.html b/docs/reference/show.brain.lut.html
index 680360c0240ffdeef1306830b74641ade30caea6..e3fdacd44eb9f8480b398e56be9cd4cfb2de00a6 100644
--- a/docs/reference/show.brain.lut.html
+++ b/docs/reference/show.brain.lut.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -114,6 +114,7 @@
 
     <pre class="usage"><span class='fu'>show.brain.lut</span>(
   <span class='no'>n</span>,
+  <span class='no'>LUTdir</span>,
   <span class='kw'>lut</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'><a href='read.tree.html'>read.tree</a></span>(),
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"verbose"</span>),
@@ -128,6 +129,10 @@
       <th>n</th>
       <td><p>number of cuts the table should have</p></td>
     </tr>
+    <tr>
+      <th>LUTdir</th>
+      <td><p>directory where to look for LUT files</p></td>
+    </tr>
     <tr>
       <th>lut</th>
       <td><p>alternative LUT, see description</p></td>
@@ -166,7 +171,7 @@ matrix (3 rows or columns) or a complete file path</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
-  <span class='fu'>show.brain.lut</span>(<span class='fl'>10</span>)
+  <span class='fu'>show.brain.lut</span>(<span class='fl'>10</span>, <span class='st'>'luts'</span>)
 }</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/show.colmat.html b/docs/reference/show.colmat.html
index 7e0dce0476b60a2abe43b1cba9560b815456e5ef..64ecf050974f7931bbff416f1eb449b8b56f90fd 100644
--- a/docs/reference/show.colmat.html
+++ b/docs/reference/show.colmat.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/show.cut.html b/docs/reference/show.cut.html
index a364b168059465e3f79ff398be95a2556ca04257..bb0a84d69683aaf256e7c3a48a1519b1c3eb9ee8 100644
--- a/docs/reference/show.cut.html
+++ b/docs/reference/show.cut.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/show.hue.range.html b/docs/reference/show.hue.range.html
index 0c11da210718841f8b819eb23830e757eddaabae..e91fba6c8f49270a310a180d966eae34264de117 100644
--- a/docs/reference/show.hue.range.html
+++ b/docs/reference/show.hue.range.html
@@ -73,7 +73,7 @@ shows the unordered colors of one in a single row of rectangles." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -155,6 +155,10 @@ shows the unordered colors of one in a single row of rectangles.</p>
       <th>v.scale</th>
       <td><p>relative vertical scaling to adjust rectangles' height</p></td>
     </tr>
+    <tr>
+      <th>show.idx</th>
+      <td><p>add index (if boolean) or specified values (if char, numeric)</p></td>
+    </tr>
     <tr>
       <th>...</th>
       <td><p>ignored</p></td>
diff --git a/docs/reference/show.lut.html b/docs/reference/show.lut.html
index b67e8bd957661edcc5c05ed26970f7e0ba0a1cfd..1c2110d63ee34278442919a5890d200de9e9ecc6 100644
--- a/docs/reference/show.lut.html
+++ b/docs/reference/show.lut.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/show.shades.html b/docs/reference/show.shades.html
index 59cde085a5872a21bee416728e37e207660f91cf..5a81234262555e2988aeb5d9fd9bd127050fe3a3 100644
--- a/docs/reference/show.shades.html
+++ b/docs/reference/show.shades.html
@@ -73,7 +73,7 @@ the number of shades for each main color (and, thus, the number of main colors.)
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/show.sub.tables.html b/docs/reference/show.sub.tables.html
index 2aea0677f2907cd6de655c4ada4b66d5943a5da4..4f26d8611dcedc7030e1cfcf91ac1452ea5b287b 100644
--- a/docs/reference/show.sub.tables.html
+++ b/docs/reference/show.sub.tables.html
@@ -74,7 +74,7 @@ They are used to trace clustering trees." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/subtables.html b/docs/reference/subtables.html
new file mode 100644
index 0000000000000000000000000000000000000000..e83e81a3a2fb23e0705dc407f0c8579138aa9165
--- /dev/null
+++ b/docs/reference/subtables.html
@@ -0,0 +1,221 @@
+<!-- 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>subtables — subtables • clusterLUTs</title>
+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/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="subtables — subtables" />
+<meta property="og:description" content="accessor function to 'sub.tables' attribute of tree.ranges." />
+
+
+
+
+<!-- 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 data-spy="scroll" data-target="#toc">
+    <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">clusterLUTs</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</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>subtables</h1>
+    
+    <div class="hidden name"><code>subtables.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>accessor function to 'sub.tables' attribute of <code>tree.ranges</code>.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>subtables</span>(<span class='no'>tr</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>tr</th>
+      <td><p>arbitrary object</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>ignored</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>'sub.tables' attribute of <code>tr</code>, if present, failure otherwise</p>
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>Return 'sub.tables' attribute of <code>tr</code>, if present, failure otherwise.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>subtables</span>(<span class='fu'><a href='tree.ranges.html'>tree.ranges</a></span>(<span class='fu'><a href='dummy.tree.html'>dummy.tree</a></span>()))</div><div class='output co'>#&gt; $`3`
+#&gt; $`3`[[1]]
+#&gt; 
+#&gt; 1 2 3 
+#&gt; 4 1 4 
+#&gt; 
+#&gt; 
+#&gt; $`6`
+#&gt; $`6`[[1]]
+#&gt; 
+#&gt; 1 6 
+#&gt; 3 1 
+#&gt; 
+#&gt; $`6`[[2]]
+#&gt; 
+#&gt; 2 
+#&gt; 1 
+#&gt; 
+#&gt; $`6`[[3]]
+#&gt; 
+#&gt; 3 4 5 
+#&gt; 1 2 1 
+#&gt; 
+#&gt; 
+#&gt; $`9`
+#&gt; $`9`[[1]]
+#&gt; 
+#&gt; 1 4 6 
+#&gt; 1 1 1 
+#&gt; 
+#&gt; $`9`[[2]]
+#&gt; 
+#&gt; 2 
+#&gt; 1 
+#&gt; 
+#&gt; $`9`[[3]]
+#&gt; 
+#&gt; 3 
+#&gt; 1 
+#&gt; 
+#&gt; $`9`[[4]]
+#&gt; 
+#&gt; 5 9 
+#&gt; 1 1 
+#&gt; 
+#&gt; $`9`[[5]]
+#&gt; 
+#&gt; 7 
+#&gt; 1 
+#&gt; 
+#&gt; $`9`[[6]]
+#&gt; 
+#&gt; 8 
+#&gt; 1 
+#&gt; 
+#&gt; </div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Benno Pütz.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/reference/tbl2mat.html b/docs/reference/tbl2mat.html
index 070bfca72d0555632372bf268ce0cfec4998c87d..bcc42959f7b287387c3760b195b0b7c8d28989d9 100644
--- a/docs/reference/tbl2mat.html
+++ b/docs/reference/tbl2mat.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/tree.ranges.html b/docs/reference/tree.ranges.html
index a3c30fb0547bc265a4474b8563aec0af26b6a15b..df45d4dfa7d35826154f82864d7cf1081c0e1797 100644
--- a/docs/reference/tree.ranges.html
+++ b/docs/reference/tree.ranges.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/tree.ranges.plot.html b/docs/reference/tree.ranges.plot.html
index b17d8b1ffd3d0fbd0045a9646cbc7aaff2f98582..cb34c2f3436d548a5f5b19b5374afad1f00384fb 100644
--- a/docs/reference/tree.ranges.plot.html
+++ b/docs/reference/tree.ranges.plot.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/treeluts.html b/docs/reference/treeluts.html
index 57ffc275ca1ee949e5f336054407d652470f3729..09e27f9edb2e69e4cc315c3fe11d2f1d7142d30c 100644
--- a/docs/reference/treeluts.html
+++ b/docs/reference/treeluts.html
@@ -40,8 +40,8 @@
 
 
 <meta property="og:title" content="LUT generation for hierarchical clustering tree — treeluts" />
-<meta property="og:description" content="Main function of this package.
-clusters defines the cluster assignments per cut. The number of clusters
+<meta property="og:description" content="Main function of this package: clusters defines the cluster assignments
+per cut. The number of clusters
 is taken from the unique values per column (need not be regular)." />
 
 
@@ -74,7 +74,7 @@ is taken from the unique values per column (need not be regular)." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -111,14 +111,14 @@ is taken from the unique values per column (need not be regular)." />
     </div>
 
     <div class="ref-description">
-    <p>Main function of this package.
-<code>clusters</code> defines the cluster assignments per cut. The number of clusters
+    <p>Main function of this package: <code>clusters</code> defines the cluster assignments
+per cut. The number of clusters
 is taken from the unique values per column (need not be regular).</p>
     </div>
 
     <pre class="usage"><span class='fu'>treeluts</span>(
   <span class='kw'>clusters</span> <span class='kw'>=</span> <span class='fu'><a href='read.tree.html'>read.tree</a></span>(),
-  <span class='kw'>outdir</span> <span class='kw'>=</span> <span class='fu'>LUTdir</span>(),
+  <span class='kw'>outdir</span> <span class='kw'>=</span> <span class='st'>"luts"</span>,
   <span class='kw'>basename</span> <span class='kw'>=</span> <span class='st'>"lut"</span>,
   <span class='kw'>lut.length</span> <span class='kw'>=</span> <span class='fl'>256</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"verbose"</span>),
@@ -156,7 +156,7 @@ is taken from the unique values per column (need not be regular).</p>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>a vector with the number of color entries per LUT generated</p>
+    <p>a vector with the number of color entries per LUT generated (invisibly)</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     
@@ -165,8 +165,10 @@ is taken from the unique values per column (need not be regular).</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/base/Random.html'>set.seed</a></span>(<span class='fl'>42</span>)
-<span class='fu'>treeluts</span>(<span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>cbind</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fl'>1</span>:<span class='fl'>5</span>,<span class='fl'>20</span>,<span class='fl'>TRUE</span>),<span class='fl'>1</span>:<span class='fl'>20</span>), <span class='fu'><a href='https://rdrr.io/r/base/tempfile.html'>tempdir</a></span>(), <span class='st'>"exmpl"</span>, <span class='kw'>verbose</span><span class='kw'>=</span><span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; /var/folders/n9/yqnj10ts5yxb142bkvkym168n7typ4/T//Rtmpiqcrxm/exmpl005.lut 
-#&gt; /var/folders/n9/yqnj10ts5yxb142bkvkym168n7typ4/T//Rtmpiqcrxm/exmpl020.lut </div></pre>
+<span class='fu'>treeluts</span>(<span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>cbind</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fl'>1</span>:<span class='fl'>5</span>,<span class='fl'>20</span>,<span class='fl'>TRUE</span>),<span class='fl'>1</span>:<span class='fl'>20</span>), <span class='fu'><a href='https://rdrr.io/r/base/tempfile.html'>tempdir</a></span>(), <span class='st'>"exmpl"</span>, <span class='kw'>verbose</span><span class='kw'>=</span><span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; /var/folders/n9/yqnj10ts5yxb142bkvkym168n7typ4/T//RtmpThyQeo/exmpl005.lut 
+#&gt; /var/folders/n9/yqnj10ts5yxb142bkvkym168n7typ4/T//RtmpThyQeo/exmpl020.lut </div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
+ <span class='fu'>treeluts</span>(<span class='kw'>outdir</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/path.expand.html'>path.expand</a></span>(<span class='st'>"~/Work/4philipp/BrainLUTs/luts"</span>),  <span class='kw'>verbose</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
+}</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/reference/vec2hsv.html b/docs/reference/vec2hsv.html
index a1a0b3f09cd15251c7d553ac43116697eef1d98c..4acea8748ca11f69c86bb3caeebcf8eff69de3c0 100644
--- a/docs/reference/vec2hsv.html
+++ b/docs/reference/vec2hsv.html
@@ -73,7 +73,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -131,10 +131,11 @@
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>an RGB vector representing the color</p>
+    <p>an RGB vector (1-column color matrix) representing the color</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>Rather than returning a hex representaion as done in <code><a href='https://rdrr.io/r/grDevices/hsv.html'>hsv</a></code>.</p>
+    <p>Rather than returning a hex representation as done in <code><a href='https://rdrr.io/r/grDevices/hsv.html'>hsv</a></code>, a
+conversion to RGB is performed before returning.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># convert RGB colors to HSV and back</span>
diff --git a/docs/reference/vec2rgb.html b/docs/reference/vec2rgb.html
index b99fc72a1a976e74304d8e94000e0e83a5dfb22d..79efa5236c69e2bbe2cc8ae63b44b96546ff06c5 100644
--- a/docs/reference/vec2rgb.html
+++ b/docs/reference/vec2rgb.html
@@ -73,7 +73,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
diff --git a/docs/reference/vlevels.html b/docs/reference/vlevels.html
index 27666cb44929e3d1c582b6f8cd6dfbf10fb58606..0ccd02601c8835f69f53811f719045c37c3b7e78 100644
--- a/docs/reference/vlevels.html
+++ b/docs/reference/vlevels.html
@@ -40,7 +40,7 @@
 
 
 <meta property="og:title" content="vector levels — vlevels" />
-<meta property="og:description" content="count the number of unique entries in vector (usually an index vector with
+<meta property="og:description" content="Count the number of unique entries in vector (usually an index vector with
 integer elements)" />
 
 
@@ -73,7 +73,7 @@ integer elements)" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>
 
@@ -110,7 +110,7 @@ integer elements)" />
     </div>
 
     <div class="ref-description">
-    <p>count the number of unique entries in vector (usually an index vector with
+    <p>Count the number of unique entries in vector (usually an index vector with
 integer elements)</p>
     </div>
 
diff --git a/docs/reference/writelut.html b/docs/reference/writelut.html
index 54d6973751d4efc4207f007e88f56c3183c61acb..a08212afc918cd60bed754341eaa6c3a613bebc4 100644
--- a/docs/reference/writelut.html
+++ b/docs/reference/writelut.html
@@ -73,7 +73,7 @@ Implemented with Rcpp to allow writing bytes." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">clusterLUTs</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0</span>
       </span>
     </div>