@@ -1,4 +1,4 @@

-<a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width=240 align="right" style="border:2px solid black;" ></a>

+# Make Complex Heatmaps <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width=240 align="right" style="border:2px solid black;" ></a>

 [![Build Status](https://travis-ci.org/jokergoo/ComplexHeatmap.svg)](https://travis-ci.org/jokergoo/ComplexHeatmap) 

 [![codecov](https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg)](https://codecov.io/github/jokergoo/ComplexHeatmap) 

@@ -8,26 +8,25 @@

 <img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="600">

-## Make Complex Heatmaps

 Complex heatmaps are efficient to visualize associations between different

 sources of data sets and reveal potential patterns. Here the

 **ComplexHeatmap** package provides a highly flexible way to arrange multiple

 heatmaps and supports various annotation graphics.

-### Citation

+## Citation

 Zuguang Gu, Roland Eils and Matthias Schlesner, [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016

-### Documentation

+## Documentation

-The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/.

+The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap.

-### Install

+## Install

 `ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by:

-```{r}

+```r

 if (!requireNamespace("BiocManager", quietly=TRUE))

     install.packages("BiocManager")

 BiocManager::install("ComplexHeatmap")

@@ -35,62 +34,62 @@ BiocManager::install("ComplexHeatmap")

 If you want the latest version, install it directly from GitHub:

-```{r}

+```r

 library(devtools)

 install_github("jokergoo/ComplexHeatmap")

 ```

-### Usage

+## Usage

 Make a single heatmap:

-```{r}

+```r

 Heatmap(mat, ...)

 ```

 A single Heatmap with column annotations:

-```{r}

+```r

 ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)

 Heatmap(mat, ..., top_annotation = ha)

 ```

 Make a list of heatmaps:

-```{r}

+```r

 Heatmap(mat1, ...) + Heatmap(mat2, ...)

 ```

 Make a list of heatmaps and row annotations:

-```{r}

+```r

 ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")

 Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha

 ```

-### Examples

+## Examples

-#### Visualize Methylation Profile with Complex Annotations

+### Visualize Methylation Profile with Complex Annotations

 ![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png)

-#### Correlations between methylation, expression and other genomic features

+### Correlations between methylation, expression and other genomic features

 ![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png)

-#### Visualize Cell Heterogeneity from Single Cell RNASeq

+### Visualize Cell Heterogeneity from Single Cell RNASeq

 ![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png)

-#### Making Enhanced OncoPrint

+### Making Enhanced OncoPrint

 ![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png)

-#### UpSet plot

+### UpSet plot

-![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg:large)

+![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg)

-### License

+## License

 MIT @ Zuguang Gu

@@ -21,4 +21,4 @@ if(file.exists(".Rbuildignore")) {

 ^pkgdown$", ".Rbuildignore")

 }

-pkgdown::build_site()

+pkgdown::build_site(run_dont_run = TRUE)

@@ -67,7 +67,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -67,7 +67,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -31,7 +31,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -96,7 +96,8 @@

 %\VignetteEngine{knitr}

 %\VignetteIndexEntry{ComplexHeatmap vignette}

 -->

-<p>Please go to <a href="http://jokergoo.github.io/ComplexHeatmap-reference/book/" class="uri">http://jokergoo.github.io/ComplexHeatmap-reference/book/</a> for the full vignette.</p>

+

+<p>Please go to <a href="http://jokergoo.github.io/ComplexHeatmap-reference/book/">http://jokergoo.github.io/ComplexHeatmap-reference/book/</a> for the full vignette.</p>

   </div>

   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

@@ -67,7 +67,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -31,7 +31,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -96,6 +96,7 @@

 %\VignetteEngine{knitr}

 %\VignetteIndexEntry{Most probably asked questions}

 -->

+

 <div id="most-probably-asked-questions" class="section level2">

 <h2 class="hasAnchor">

 <a href="#most-probably-asked-questions" class="anchor"></a>Most probably asked questions</h2>

@@ -107,40 +108,40 @@ h1, h2, h3, h4, h5 {

 <div id="there-is-no-plot-comming-out-after-running-heatmap-function-" class="section level3">

 <h3 class="hasAnchor">

 <a href="#there-is-no-plot-comming-out-after-running-heatmap-function-" class="anchor"></a>There is no plot comming out after running Heatmap() function.</h3>

-<p>In this case, you need to use <code><a href="../reference/draw-dispatch.html">draw()</a></code> function explicitly. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap</a> and <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#plot-the-heamtap-list" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#plot-the-heamtap-list</a>.</p>

+<p>In this case, you need to use <code><a href="../reference/draw-dispatch.html">draw()</a></code> function explicitly. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#plot-the-heatmap</a> and <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#plot-the-heamtap-list">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#plot-the-heamtap-list</a>.</p>

 </div>

 <div id="retrieve-orders-and-dendrograms-" class="section level3">

 <h3 class="hasAnchor">

 <a href="#retrieve-orders-and-dendrograms-" class="anchor"></a>Retrieve orders and dendrograms.</h3>

-<p>For retrieving orders and dendrograms from a single heatmap. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap</a>.</p>

-<p>For retrieving orders and dendrograms from a list of heatmaps. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms-from-a-list-of-heatmaps" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms-from-a-list-of-heatmaps</a>.</p>

+<p>For retrieving orders and dendrograms from a single heatmap. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#get-orders-and-dendrograms-from-heatmap</a>.</p>

+<p>For retrieving orders and dendrograms from a list of heatmaps. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms-from-a-list-of-heatmaps">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#get-orders-and-dendrograms-from-a-list-of-heatmaps</a>.</p>

 </div>

 <div id="how-should-i-control-the-height-or-width-of-the-heatmap-annotations" class="section level3">

 <h3 class="hasAnchor">

 <a href="#how-should-i-control-the-height-or-width-of-the-heatmap-annotations" class="anchor"></a>How should I control the height or width of the heatmap annotations?</h3>

-<p>For complex annotations generated by <code>anno_*()</code> functions, width or height should be set inside the <code>anno_*()</code> function, such as <code><a href="../reference/anno_points.html">anno_points(..., height = ...)</a></code>. The size of simple annotations is controlled by <code>anno_simple_size</code>. The <code>width</code>/<code>height</code> and <code>annotation_width</code>/<code>annotation_height</code> are used to adjust the size for multiple annotations which are put in one <code>HeatmapAnnotation</code> object. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#multiple-annotations" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#multiple-annotations</a></p>

+<p>For complex annotations generated by <code>anno_*()</code> functions, width or height should be set inside the <code>anno_*()</code> function, such as <code><a href="../reference/anno_points.html">anno_points(..., height = ...)</a></code>. The size of simple annotations is controlled by <code>anno_simple_size</code>. The <code>width</code>/<code>height</code> and <code>annotation_width</code>/<code>annotation_height</code> are used to adjust the size for multiple annotations which are put in one <code>HeatmapAnnotation</code> object. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#multiple-annotations">https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#multiple-annotations</a></p>

 </div>

 <div id="how-should-i-control-the-axes-of-the-annotations" class="section level3">

 <h3 class="hasAnchor">

 <a href="#how-should-i-control-the-axes-of-the-annotations" class="anchor"></a>How should I control the axes of the annotations?</h3>

 <p>In the annotation functions <code>anno_*()</code>, the argument <code>axis_param</code> can be used to set the axes. The value should be a list and the default settings for axis can be get by:</p>

-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/default_axis_param.html">default_axis_param</a></span>(<span class="st">"column"</span>)

-<span class="kw"><a href="../reference/default_axis_param.html">default_axis_param</a></span>(<span class="st">"row"</span>)</code></pre></div>

+<pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/default_axis_param.html">default_axis_param</a></span>(<span class="st">"column"</span>)

+<span class="kw"><a href="../reference/default_axis_param.html">default_axis_param</a></span>(<span class="st">"row"</span>)</code></pre>

 </div>

 <div id="how-to-control-the-style-of-legends" class="section level3">

 <h3 class="hasAnchor">

 <a href="#how-to-control-the-style-of-legends" class="anchor"></a>How to control the style of legends?</h3>

-<p>The style of legends can be controlled by <code>heatmap_legend_param</code> in <code><a href="../reference/Heatmap.html">Heatmap()</a></code>, or <code>annotation_legend_param</code> in <code><a href="../reference/HeatmapAnnotation.html">HeatmapAnnotation()</a></code>. The parameters for controlling legends are those arguments in <code><a href="../reference/Legend.html">Legend()</a></code> function. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#heatmap-and-annotation-legends" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#heatmap-and-annotation-legends</a>.</p>

+<p>The style of legends can be controlled by <code>heatmap_legend_param</code> in <code><a href="../reference/Heatmap.html">Heatmap()</a></code>, or <code>annotation_legend_param</code> in <code><a href="../reference/HeatmapAnnotation.html">HeatmapAnnotation()</a></code>. The parameters for controlling legends are those arguments in <code><a href="../reference/Legend.html">Legend()</a></code> function. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#heatmap-and-annotation-legends">https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#heatmap-and-annotation-legends</a>.</p>

 </div>

 <div id="some-text-are-cut-by-the-plotting-region-" class="section level3">

 <h3 class="hasAnchor">

 <a href="#some-text-are-cut-by-the-plotting-region-" class="anchor"></a>Some text are cut by the plotting region.</h3>

-<p>The layout of the <strong>ComplexHeatmap</strong> is not perfect that it is still possible some of the text are drawn out of the plotting region. In this case, you can set the <code>padding</code> argument in <code><a href="../reference/draw-dispatch.html">draw()</a></code> function to increase the blank areas around the final plot. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#manually-increase-space-around-the-plot" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#manually-increase-space-around-the-plot</a>.</p>

+<p>The layout of the <strong>ComplexHeatmap</strong> is not perfect that it is still possible some of the text are drawn out of the plotting region. In this case, you can set the <code>padding</code> argument in <code><a href="../reference/draw-dispatch.html">draw()</a></code> function to increase the blank areas around the final plot. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#manually-increase-space-around-the-plot">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#manually-increase-space-around-the-plot</a>.</p>

 </div>

 <div id="can-the-heatmaps-be-added-vertically" class="section level3">

 <h3 class="hasAnchor">

 <a href="#can-the-heatmaps-be-added-vertically" class="anchor"></a>Can the heatmaps be added vertically?</h3>

-<p>Yes, use <code><a href="../reference/pct_v_pct.html">%v%</a></code> instead of <code><a href="https://rdrr.io/r/base/Arithmetic.html">+</a></code>. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#vertical-concatenation" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#vertical-concatenation</a>.</p>

+<p>Yes, use <code><a href="../reference/pct_v_pct.html">%v%</a></code> instead of <code><a href="https://rdrr.io/r/base/Arithmetic.html">+</a></code>. See <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#vertical-concatenation">https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#vertical-concatenation</a>.</p>

 </div>

 <div id="does-heatmap-title-supports-mathematical-expression" class="section level3">

 <h3 class="hasAnchor">

@@ -151,29 +152,29 @@ h1, h2, h3, h4, h5 {

 <h3 class="hasAnchor">

 <a href="#i-have-many-heatmaps-and-i-want-to-put-them-into-different-panels-for-a-big-figure-for-my-paper-" class="anchor"></a>I have many heatmaps and I want to put them into different panels for a big figure for my paper.</h3>

 <p>You can set <code>newpage = FALSE</code> in <code><a href="../reference/draw-dispatch.html">draw()</a></code> function and use <code>grid.layout()</code> to manage the layout of your panels.</p>

-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout =</span> <span class="kw">grid.layout</span>(...)))

+<pre class="sourceCode r"><code class="sourceCode r"><span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout =</span> <span class="kw">grid.layout</span>(...)))

 <span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout.pos.row =</span> ..., <span class="dt">layout.pos.col =</span> ...))

 <span class="kw"><a href="../reference/draw-dispatch.html">draw</a></span>(ht, <span class="dt">newpage =</span> <span class="ot">FALSE</span>) <span class="co"># or draw(ht_list, newpage = FALSE)</span>

 <span class="kw">popViewport</span>()

-...</code></pre></div>

+...</code></pre>

 <p>But I more suggest to use <code>grid.grabExpr()</code> to directly capture the output of the heatmap and later draw the whole plot as a single graphic element by <code>grid.draw()</code>.</p>

-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">ht_grob =<span class="st"> </span><span class="kw">grid.grabExpr</span>(<span class="kw"><a href="../reference/draw-dispatch.html">draw</a></span>(ht, ...))

+<pre class="sourceCode r"><code class="sourceCode r">ht_grob =<span class="st"> </span><span class="kw">grid.grabExpr</span>(<span class="kw"><a href="../reference/draw-dispatch.html">draw</a></span>(ht, ...))

 <span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout =</span> <span class="kw">grid.layout</span>(...)))

 <span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout.pos.row =</span> ..., <span class="dt">layout.pos.col =</span> ...))

 <span class="kw">grid.draw</span>(ht_grob)

 <span class="kw">popViewport</span>()

-...</code></pre></div>

+...</code></pre>

 </div>

 <div id="i-have-a-matrix-with-too-many-rows-and-i-want-to-simplify-the-row-dendrogram-" class="section level3">

 <h3 class="hasAnchor">

 <a href="#i-have-a-matrix-with-too-many-rows-and-i-want-to-simplify-the-row-dendrogram-" class="anchor"></a>I have a matrix with too many rows and I want to simplify the row dendrogram.</h3>

 <p>You can first group your rows into several groups and make a group-level dendrogram on it. See following example:</p>

-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="dv">1000</span><span class="op">*</span><span class="dv">10</span>), <span class="dt">nr =</span> <span class="dv">1000</span>)

+<pre class="sourceCode r"><code class="sourceCode r">m =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="dv">1000</span>*<span class="dv">10</span>), <span class="dt">nr =</span> <span class="dv">1000</span>)

 hc =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/stats/hclust.html">hclust</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/dist.html">dist</a></span>(m))

 group =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/stats/cutree.html">cutree</a></span>(hc, <span class="dt">k =</span> <span class="dv">6</span>)

 <span class="kw"><a href="../reference/Heatmap.html">Heatmap</a></span>(m, <span class="dt">cluster_rows =</span> <span class="kw"><a href="../reference/cluster_within_group.html">cluster_within_group</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/t.html">t</a></span>(m), group), 

-    <span class="dt">row_split =</span> <span class="dv">6</span>, <span class="dt">border =</span> <span class="ot">TRUE</span>) <span class="co"># it would be better if also set row_split</span></code></pre></div>

+    <span class="dt">row_split =</span> <span class="dv">6</span>, <span class="dt">border =</span> <span class="ot">TRUE</span>) <span class="co"># it would be better if also set row_split</span></code></pre>

 <p><img src="most_probably_asked_questions_files/figure-html/unnamed-chunk-6-1.png" width="700"></p>

 </div>

 <div id="i-have-a-matrix-with-huge-nunmber-of-rows-or-columns-what-is-the-efficient-way-to-visualize-it" class="section level3">

@@ -185,7 +186,7 @@ group =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/stat

 <h3 class="hasAnchor">

 <a href="#how-to-add-axes-for-dendrograms" class="anchor"></a>How to add axes for dendrograms?</h3>

 <p>You need to use <code><a href="../reference/decorate_row_dend.html">decorate_row_dend()</a></code> or <code><a href="../reference/decorate_column_dend.html">decorate_column_dend()</a></code> to manually add the axes. See following examples:</p>

-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="dv">100</span>), <span class="dv">10</span>)

+<pre class="sourceCode r"><code class="sourceCode r">m =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="dv">100</span>), <span class="dv">10</span>)

 ht =<span class="st"> </span><span class="kw"><a href="../reference/Heatmap.html">Heatmap</a></span>(m, <span class="dt">name =</span> <span class="st">"foo"</span>, 

     <span class="dt">row_dend_width =</span> <span class="kw">unit</span>(<span class="dv">4</span>, <span class="st">"cm"</span>),

@@ -197,9 +198,9 @@ ht =<span class="st"> </span><span class="kw"><a href="../reference/Heatmap.html

 })

 <span class="kw"><a href="../reference/decorate_row_dend.html">decorate_row_dend</a></span>(<span class="st">"foo"</span>, {

     vp =<span class="st"> </span><span class="kw">current.viewport</span>()

-    xscale =<span class="st"> </span>vp<span class="op">$</span>xscale

-    <span class="kw">grid.xaxis</span>(<span class="dt">at =</span> xscale[<span class="dv">2</span>] <span class="op">-</span><span class="st"> </span><span class="dv">0</span><span class="op">:</span><span class="dv">5</span>, <span class="dt">label =</span> <span class="dv">0</span><span class="op">:</span><span class="dv">5</span>)

-})</code></pre></div>

+    xscale =<span class="st"> </span>vp$xscale

+    <span class="kw">grid.xaxis</span>(<span class="dt">at =</span> xscale[<span class="dv">2</span>] -<span class="st"> </span><span class="dv">0</span>:<span class="dv">5</span>, <span class="dt">label =</span> <span class="dv">0</span>:<span class="dv">5</span>)

+})</code></pre>

 <p><img src="most_probably_asked_questions_files/figure-html/unnamed-chunk-7-1.png" width="700"></p>

 <p>Note for the left row dendrogram, the x-axis is from right to left, you need to self-define <code>at</code> and <code>label</code> in <code>grid.xaxis()</code> function.</p>

 <p>You can also check <code><a href="../reference/annotation_axis_grob.html">annotation_axis_grob()</a></code> function (later use <code>grid.draw()</code> to draw the axes) to draw a nicer axis.</p>

@@ -217,19 +218,19 @@ ht =<span class="st"> </span><span class="kw"><a href="../reference/Heatmap.html

 <h3 class="hasAnchor">

 <a href="#i-only-want-to-draw-dendrograms-plus-a-list-of-annotations-" class="anchor"></a>I only want to draw dendrograms plus a list of annotations.</h3>

 <p>You need to assign the dendrograms to a zero-row/column matrix:</p>

-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">hc =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/stats/hclust.html">hclust</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/dist.html">dist</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="dv">100</span>), <span class="dv">10</span>)))

+<pre class="sourceCode r"><code class="sourceCode r">hc =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/stats/hclust.html">hclust</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/dist.html">dist</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/stats/Normal.html">rnorm</a></span>(<span class="dv">100</span>), <span class="dv">10</span>)))

 <span class="kw"><a href="../reference/Heatmap.html">Heatmap</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="dt">nc =</span> <span class="dv">0</span>, <span class="dt">nr =</span> <span class="dv">10</span>), <span class="dt">cluster_rows =</span> hc, 

     <span class="dt">right_annotation =</span> <span class="kw"><a href="../reference/rowAnnotation.html">rowAnnotation</a></span>(

-        <span class="dt">foo =</span> <span class="kw"><a href="../reference/anno_points.html">anno_points</a></span>(<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>),

-        <span class="dt">sth =</span> <span class="dv">1</span><span class="op">:</span><span class="dv">10</span>,

-        <span class="dt">bar =</span> <span class="kw"><a href="../reference/anno_barplot.html">anno_barplot</a></span>(<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>)),

-    <span class="dt">row_split =</span> <span class="dv">2</span>)</code></pre></div>

+        <span class="dt">foo =</span> <span class="kw"><a href="../reference/anno_points.html">anno_points</a></span>(<span class="dv">1</span>:<span class="dv">10</span>),

+        <span class="dt">sth =</span> <span class="dv">1</span>:<span class="dv">10</span>,

+        <span class="dt">bar =</span> <span class="kw"><a href="../reference/anno_barplot.html">anno_barplot</a></span>(<span class="dv">1</span>:<span class="dv">10</span>)),

+    <span class="dt">row_split =</span> <span class="dv">2</span>)</code></pre>

 <p><img src="most_probably_asked_questions_files/figure-html/unnamed-chunk-8-1.png" width="700"></p>

 </div>

 <div id="i-still-have-a-problem-with-the-package-and-i-am-lost-in-the-ocean-of-the-huge-vignette-" class="section level3">

 <h3 class="hasAnchor">

 <a href="#i-still-have-a-problem-with-the-package-and-i-am-lost-in-the-ocean-of-the-huge-vignette-" class="anchor"></a>I still have a problem with the package and I am lost in the ocean of the huge vignette.</h3>

-<p>The vignette (<a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/</a>) contains huge number of examples and plots showing different usage of the package. It is sometimes not easy to find the solution you are looking for. In this case, don’t hesitate to write me an email. I am glad to answer all of your questions!</p>

+<p>The vignette (<a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/">https://jokergoo.github.io/ComplexHeatmap-reference/book/</a>) contains huge number of examples and plots showing different usage of the package. It is sometimes not easy to find the solution you are looking for. In this case, don’t hesitate to write me an email. I am glad to answer all of your questions!</p>

 </div>

 </div>

   </div>

Binary files a/docs/articles/most_probably_asked_questions_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/most_probably_asked_questions_files/figure-html/unnamed-chunk-6-1.png differ

Binary files a/docs/articles/most_probably_asked_questions_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/most_probably_asked_questions_files/figure-html/unnamed-chunk-7-1.png differ

Binary files a/docs/articles/most_probably_asked_questions_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/most_probably_asked_questions_files/figure-html/unnamed-chunk-8-1.png differ

@@ -67,7 +67,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -34,7 +34,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -84,85 +84,78 @@

       </header><div class="row">

   <div class="contents col-md-9">

+<div id="make-complex-heatmaps" class="section level1">

+<div class="page-header"><h1 class="hasAnchor">

+<a href="#make-complex-heatmaps" class="anchor"></a>Make Complex Heatmaps <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width="240" align="right" style="border:2px solid black;"></a>

+</h1></div>

-

-<p><a href="https://travis-ci.org/jokergoo/ComplexHeatmap"><img src="https://travis-ci.org/jokergoo/ComplexHeatmap.svg" alt="Build Status"></a> <a href="https://codecov.io/github/jokergoo/ComplexHeatmap"><img src="https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg" alt="codecov"></a> <a href="https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/"><img src="http://www.bioconductor.org/shields/downloads/devel/ComplexHeatmap.svg" alt="bioc"></a> <a href="https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/"><embed src="http://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap&amp;"></embed></a> <a href="http://bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html"><img src="http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg" alt="bioc"></a></p>

 <p><img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="600"></p>

-<div id="make-complex-heatmaps" class="section level2">

-<h2 class="hasAnchor">

-<a href="#make-complex-heatmaps" class="anchor"></a>Make Complex Heatmaps</h2>

 <p>Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the <strong>ComplexHeatmap</strong> package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.</p>

-<div id="citation" class="section level3">

-<h3 class="hasAnchor">

-<a href="#citation" class="anchor"></a>Citation</h3>

+<div id="citation" class="section level2">

+<h2 class="hasAnchor">

+<a href="#citation" class="anchor"></a>Citation</h2>

 <p>Zuguang Gu, Roland Eils and Matthias Schlesner, <a href="http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract">Complex heatmaps reveal patterns and correlations in multidimensional genomic data</a>, Bioinformatics, 2016</p>

 </div>

-<div id="documentation" class="section level3">

-<h3 class="hasAnchor">

-<a href="#documentation" class="anchor"></a>Documentation</h3>

-<p>The full documentations are available at <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/" class="uri">https://jokergoo.github.io/ComplexHeatmap-reference/book/</a>.</p>

+<div id="documentation" class="section level2">

+<h2 class="hasAnchor">

+<a href="#documentation" class="anchor"></a>Documentation</h2>

+<p>The full documentations are available at <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/">https://jokergoo.github.io/ComplexHeatmap-reference/book/</a>.</p>

 </div>

-<div id="install" class="section level3">

-<h3 class="hasAnchor">

-<a href="#install" class="anchor"></a>Install</h3>

+<div id="install" class="section level2">

+<h2 class="hasAnchor">

+<a href="#install" class="anchor"></a>Install</h2>

 <p><code>ComplexHeatmap</code> is available on <a href="http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html">Bioconductor</a>, you can install it by:</p>

-<pre class="{r}"><code>if (!requireNamespace("BiocManager", quietly=TRUE))

-    install.packages("BiocManager")

-BiocManager::install("ComplexHeatmap")</code></pre>

+<p><code>{r} if (!requireNamespace("BiocManager", quietly=TRUE))     install.packages("BiocManager") BiocManager::install("ComplexHeatmap")</code></p>

 <p>If you want the latest version, install it directly from GitHub:</p>

-<pre class="{r}"><code><a href="https://rdrr.io/r/base/library.html">library(devtools)

-install_github("jokergoo/ComplexHeatmap")</a></code></pre>

+<p><code>{r} library(devtools) install_github("jokergoo/ComplexHeatmap")</code></p>

 </div>

-<div id="usage" class="section level3">

-<h3 class="hasAnchor">

-<a href="#usage" class="anchor"></a>Usage</h3>

+<div id="usage" class="section level2">

+<h2 class="hasAnchor">

+<a href="#usage" class="anchor"></a>Usage</h2>

 <p>Make a single heatmap:</p>

-<pre class="{r}"><code><a href="reference/Heatmap.html">Heatmap(mat, ...)</a></code></pre>

+<p><code>{r} Heatmap(mat, ...)</code></p>

 <p>A single Heatmap with column annotations:</p>

-<pre class="{r}"><code>ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)

-Heatmap(mat, ..., top_annotation = ha)</code></pre>

+<p><code>{r} ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...) Heatmap(mat, ..., top_annotation = ha)</code></p>

 <p>Make a list of heatmaps:</p>

-<pre class="{r}"><code>Heatmap(mat1, ...) + Heatmap(mat2, ...)</code></pre>

+<p><code>{r} Heatmap(mat1, ...) + Heatmap(mat2, ...)</code></p>

 <p>Make a list of heatmaps and row annotations:</p>

-<pre class="{r}"><code>ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")

-Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha</code></pre>

+<p><code>{r} ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row") Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha</code></p>

 </div>

-<div id="examples" class="section level3">

+<div id="examples" class="section level2">

+<h2 class="hasAnchor">

+<a href="#examples" class="anchor"></a>Examples</h2>

+<div id="visualize-methylation-profile-with-complex-annotations" class="section level3">

 <h3 class="hasAnchor">

-<a href="#examples" class="anchor"></a>Examples</h3>

-<div id="visualize-methylation-profile-with-complex-annotations" class="section level4">

-<h4 class="hasAnchor">

-<a href="#visualize-methylation-profile-with-complex-annotations" class="anchor"></a>Visualize Methylation Profile with Complex Annotations</h4>

+<a href="#visualize-methylation-profile-with-complex-annotations" class="anchor"></a>Visualize Methylation Profile with Complex Annotations</h3>

 <p><img src="https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png" alt="complexheatmap_example4"></p>

 </div>

-<div id="correlations-between-methylation-expression-and-other-genomic-features" class="section level4">

-<h4 class="hasAnchor">

-<a href="#correlations-between-methylation-expression-and-other-genomic-features" class="anchor"></a>Correlations between methylation, expression and other genomic features</h4>

+<div id="correlations-between-methylation-expression-and-other-genomic-features" class="section level3">

+<h3 class="hasAnchor">

+<a href="#correlations-between-methylation-expression-and-other-genomic-features" class="anchor"></a>Correlations between methylation, expression and other genomic features</h3>

 <p><img src="https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png" alt="complexheatmap_example3"></p>

 </div>

-<div id="visualize-cell-heterogeneity-from-single-cell-rnaseq" class="section level4">

-<h4 class="hasAnchor">

-<a href="#visualize-cell-heterogeneity-from-single-cell-rnaseq" class="anchor"></a>Visualize Cell Heterogeneity from Single Cell RNASeq</h4>

+<div id="visualize-cell-heterogeneity-from-single-cell-rnaseq" class="section level3">

+<h3 class="hasAnchor">

+<a href="#visualize-cell-heterogeneity-from-single-cell-rnaseq" class="anchor"></a>Visualize Cell Heterogeneity from Single Cell RNASeq</h3>

 <p><img src="https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png" alt="complexheatmap_example2"></p>

 </div>

-<div id="making-enhanced-oncoprint" class="section level4">

-<h4 class="hasAnchor">

-<a href="#making-enhanced-oncoprint" class="anchor"></a>Making Enhanced OncoPrint</h4>

+<div id="making-enhanced-oncoprint" class="section level3">

+<h3 class="hasAnchor">

+<a href="#making-enhanced-oncoprint" class="anchor"></a>Making Enhanced OncoPrint</h3>

 <p><img src="https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png" alt="complexheatmap_example1"></p>

 </div>

-<div id="upset-plot" class="section level4">

-<h4 class="hasAnchor">

-<a href="#upset-plot" class="anchor"></a>UpSet plot</h4>

-<p><embed src="https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg:large"></embed></p>

+<div id="upset-plot" class="section level3">

+<h3 class="hasAnchor">

+<a href="#upset-plot" class="anchor"></a>UpSet plot</h3>

+<p><img src="https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg"></p>

 </div>

 </div>

-<div id="license" class="section level3">

-<h3 class="hasAnchor">

-<a href="#license" class="anchor"></a>License</h3>

+<div id="license" class="section level2">

+<h2 class="hasAnchor">

+<a href="#license" class="anchor"></a>License</h2>

 <p>MIT @ Zuguang Gu</p>

 </div>

 </div>

-

   </div>

   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

@@ -199,7 +192,11 @@ Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha</code></pre>

   <div class="dev-status">

 <h2>Dev status</h2>

 <ul class="list-unstyled">

-<li><a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width="240" align="right" style="border:2px solid black;"></a></li>

+<li><a href="https://travis-ci.org/jokergoo/ComplexHeatmap"><img src="https://travis-ci.org/jokergoo/ComplexHeatmap.svg" alt="Build Status"></a></li>

+<li><a href="https://codecov.io/github/jokergoo/ComplexHeatmap"><img src="https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg" alt="codecov"></a></li>

+<li><a href="https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/"><img src="http://www.bioconductor.org/shields/downloads/devel/ComplexHeatmap.svg" alt="bioc"></a></li>

+<li><a href="https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/"><embed src="http://mcube.nju.edu.cn/cgi-bin/zuguanggu/bioc_download.pl?package=ComplexHeatmap&amp;"></embed></a></li>

+<li><a href="http://bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html"><img src="http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg" alt="bioc"></a></li>

 </ul>

 </div>

 </div>

@@ -1,4 +1,4 @@

-pandoc: 1.19.2.1

+pandoc: 1.12.3.1

 pkgdown: 1.4.1

 pkgdown_sha: ~

 articles:

@@ -69,7 +69,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -139,8 +139,7 @@ method and the <code>%v%v</code> method so that above three classes can be appen

     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>

     <pre class="examples"><div class='input'><span class='co'># There is no example</span>

-<span class='kw'>NULL</span></div><div class='output co'>#&gt; NULL</div><div class='input'>

-</div></pre>

+<span class='kw'>NULL</span></div><div class='output co'>#&gt; NULL</div></pre>

   </div>

   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

     <h2>Contents</h2>

@@ -8,11 +8,13 @@

 <title>Class for Concatenating Heatmaps and Annotations — AdditiveUnit-class • ComplexHeatmap</title>

+

 <!-- jquery -->

 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>

 <!-- Bootstrap -->

 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />

+

 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>

 <!-- Font Awesome icons -->

@@ -32,13 +34,14 @@

-<meta property="og:title" content="Class for Concatenating Heatmaps and Annotations — AdditiveUnit-class" />

+<meta property="og:title" content="Class for Concatenating Heatmaps and Annotations — AdditiveUnit-class" />

 <meta property="og:description" content="Class for Concatenating Heatmaps and Annotations" />

 <meta name="twitter:card" content="summary" />

+

 <!-- mathjax -->

 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>

 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>

@@ -66,7 +69,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -97,7 +100,6 @@

   </ul>

 </li>

       </ul>

-      

       <ul class="nav navbar-nav navbar-right">

         <li>

   <a href="https://github.com/jokergoo/ComplexHeatmap">

@@ -124,18 +126,16 @@

     </div>

     <div class="ref-description">

-    

     <p>Class for Concatenating Heatmaps and Annotations</p>

-    

     </div>

-        

+

+

     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

     <p>This class is a super class for <code><a href='Heatmap-class.rd.html'>Heatmap-class</a></code>, <code><a href='HeatmapList-class.rd.html'>HeatmapList-class</a></code> and

 <code><a href='HeatmapAnnotation-class.rd.html'>HeatmapAnnotation-class</a></code> classes. It is only designed for <code>+</code> generic

 method and the <code>%v%v</code> method so that above three classes can be appended to each other.</p>

-    

     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>

     <pre class="examples"><div class='input'><span class='co'># There is no example</span>

@@ -145,9 +145,7 @@ method and the <code>%v%v</code> method so that above three classes can be appen

   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

     <h2>Contents</h2>

     <ul class="nav nav-pills nav-stacked">

-      

       <li><a href="#details">Details</a></li>

-      

       <li><a href="#examples">Examples</a></li>

     </ul>

@@ -69,7 +69,7 @@

       </button>

       <span class="navbar-brand">

         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>

-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>

+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>

       </span>

     </div>

@@ -149,8 +149,7 @@

     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>

     <pre class="examples"><div class='input'><span class='co'># There is no example</span>

-<span class='kw'>NULL</span></div><div class='output co'>#&gt; NULL</div><div class='input'>

-</div></pre>

+<span class='kw'>NULL</span></div><div class='output co'>#&gt; NULL</div></pre>

   </div>

   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

     <h2>Contents</h2>

@@ -8,11 +8,13 @@

 <title>Constructor Method for AdditiveUnit Class — AdditiveUnit • ComplexHeatmap</title>

+

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