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><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'>#> [,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" 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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'>#> <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'><-</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" 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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 "seeded" 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">`%&%`</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'>#> $`3` +#> $`3`[[1]] +#> +#> 1 2 3 +#> 4 1 4 +#> +#> +#> $`6` +#> $`6`[[1]] +#> +#> 1 6 +#> 3 1 +#> +#> $`6`[[2]] +#> +#> 2 +#> 1 +#> +#> $`6`[[3]] +#> +#> 3 4 5 +#> 1 2 1 +#> +#> +#> $`9` +#> $`9`[[1]] +#> +#> 1 4 6 +#> 1 1 1 +#> +#> $`9`[[2]] +#> +#> 2 +#> 1 +#> +#> $`9`[[3]] +#> +#> 3 +#> 1 +#> +#> $`9`[[4]] +#> +#> 5 9 +#> 1 1 +#> +#> $`9`[[5]] +#> +#> 7 +#> 1 +#> +#> $`9`[[6]] +#> +#> 8 +#> 1 +#> +#> </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'>#> /var/folders/n9/yqnj10ts5yxb142bkvkym168n7typ4/T//Rtmpiqcrxm/exmpl005.lut -#> /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'>#> /var/folders/n9/yqnj10ts5yxb142bkvkym168n7typ4/T//RtmpThyQeo/exmpl005.lut +#> /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>