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generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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-<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>
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+# 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>
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 [![Build Status](https://travis-ci.org/jokergoo/ComplexHeatmap.svg)](https://travis-ci.org/jokergoo/ComplexHeatmap) 
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 [![codecov](https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg)](https://codecov.io/github/jokergoo/ComplexHeatmap) 
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@@ -8,26 +8,25 @@
8 8
 
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 <img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="600">
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-## Make Complex Heatmaps
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 Complex heatmaps are efficient to visualize associations between different
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 sources of data sets and reveal potential patterns. Here the
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 **ComplexHeatmap** package provides a highly flexible way to arrange multiple
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 heatmaps and supports various annotation graphics.
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-### Citation
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+## Citation
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 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
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-### Documentation
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+## Documentation
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-The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/.
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+The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap.
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-### Install
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+## Install
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 `ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by:
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-```{r}
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+```r
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 if (!requireNamespace("BiocManager", quietly=TRUE))
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     install.packages("BiocManager")
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 BiocManager::install("ComplexHeatmap")
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@@ -35,62 +34,62 @@ BiocManager::install("ComplexHeatmap")
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 If you want the latest version, install it directly from GitHub:
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-```{r}
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+```r
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 library(devtools)
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 install_github("jokergoo/ComplexHeatmap")
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 ```
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-### Usage
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+## Usage
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45 44
 Make a single heatmap:
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-```{r}
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+```r
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 Heatmap(mat, ...)
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 ```
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 A single Heatmap with column annotations:
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-```{r}
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+```r
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 ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)
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 Heatmap(mat, ..., top_annotation = ha)
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 ```
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 Make a list of heatmaps:
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-```{r}
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+```r
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 Heatmap(mat1, ...) + Heatmap(mat2, ...)
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 ```
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 Make a list of heatmaps and row annotations:
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-```{r}
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+```r
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 ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")
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 Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha
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 ```
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-### Examples
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+## Examples
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-#### Visualize Methylation Profile with Complex Annotations
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+### Visualize Methylation Profile with Complex Annotations
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 ![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png)
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-#### Correlations between methylation, expression and other genomic features
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+### Correlations between methylation, expression and other genomic features
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 ![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png)
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-#### Visualize Cell Heterogeneity from Single Cell RNASeq
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+### Visualize Cell Heterogeneity from Single Cell RNASeq
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 ![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png)
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-#### Making Enhanced OncoPrint
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+### Making Enhanced OncoPrint
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 ![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png)
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-#### UpSet plot
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+### UpSet plot
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-![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg:large)
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+![](https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg)
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-### License
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+## License
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 MIT @ Zuguang Gu
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 ^pkgdown$", ".Rbuildignore")
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 }
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-pkgdown::build_site()
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+pkgdown::build_site(run_dont_run = TRUE)
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@@ -67,7 +67,7 @@
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       </span>
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     </div>
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       </span>
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     </div>
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       </span>
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     </div>
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 %\VignetteEngine{knitr}
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 %\VignetteIndexEntry{ComplexHeatmap vignette}
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 -->
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-<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>
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+
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+<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>
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   </div>
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   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       </span>
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     </div>
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       </span>
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     </div>
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 %\VignetteEngine{knitr}
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 %\VignetteIndexEntry{Most probably asked questions}
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 -->
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+
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 <div id="most-probably-asked-questions" class="section level2">
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 <h2 class="hasAnchor">
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 <a href="#most-probably-asked-questions" class="anchor"></a>Most probably asked questions</h2>
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@@ -107,40 +108,40 @@ h1, h2, h3, h4, h5 {
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 <div id="there-is-no-plot-comming-out-after-running-heatmap-function-" class="section level3">
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 <h3 class="hasAnchor">
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 <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>
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-<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>
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+<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>
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 </div>
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 <div id="retrieve-orders-and-dendrograms-" class="section level3">
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 <h3 class="hasAnchor">
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 <a href="#retrieve-orders-and-dendrograms-" class="anchor"></a>Retrieve orders and dendrograms.</h3>
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-<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>
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-<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>
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+<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>
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+<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>
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 </div>
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 <div id="how-should-i-control-the-height-or-width-of-the-heatmap-annotations" class="section level3">
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 <h3 class="hasAnchor">
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 <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>
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-<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>
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+<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>
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 </div>
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 <div id="how-should-i-control-the-axes-of-the-annotations" class="section level3">
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 <h3 class="hasAnchor">
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 <a href="#how-should-i-control-the-axes-of-the-annotations" class="anchor"></a>How should I control the axes of the annotations?</h3>
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 <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>
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-<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>)
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-<span class="kw"><a href="../reference/default_axis_param.html">default_axis_param</a></span>(<span class="st">"row"</span>)</code></pre></div>
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+<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>)
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+<span class="kw"><a href="../reference/default_axis_param.html">default_axis_param</a></span>(<span class="st">"row"</span>)</code></pre>
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 </div>
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 <div id="how-to-control-the-style-of-legends" class="section level3">
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 <h3 class="hasAnchor">
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 <a href="#how-to-control-the-style-of-legends" class="anchor"></a>How to control the style of legends?</h3>
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-<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>
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+<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>
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 </div>
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 <div id="some-text-are-cut-by-the-plotting-region-" class="section level3">
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 <h3 class="hasAnchor">
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 <a href="#some-text-are-cut-by-the-plotting-region-" class="anchor"></a>Some text are cut by the plotting region.</h3>
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-<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>
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+<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>
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 </div>
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 <div id="can-the-heatmaps-be-added-vertically" class="section level3">
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 <h3 class="hasAnchor">
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 <a href="#can-the-heatmaps-be-added-vertically" class="anchor"></a>Can the heatmaps be added vertically?</h3>
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-<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>
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+<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>
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 </div>
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 <div id="does-heatmap-title-supports-mathematical-expression" class="section level3">
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 <h3 class="hasAnchor">
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 <h3 class="hasAnchor">
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 <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>
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 <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>
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-<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>(...)))
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+<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>(...)))
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 <span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout.pos.row =</span> ..., <span class="dt">layout.pos.col =</span> ...))
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 <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>
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 <span class="kw">popViewport</span>()
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-...</code></pre></div>
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+...</code></pre>
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 <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>
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-<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, ...))
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+<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, ...))
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 <span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout =</span> <span class="kw">grid.layout</span>(...)))
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 <span class="kw">pushViewport</span>(<span class="kw">viewport</span>(<span class="dt">layout.pos.row =</span> ..., <span class="dt">layout.pos.col =</span> ...))
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 <span class="kw">grid.draw</span>(ht_grob)
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 <span class="kw">popViewport</span>()
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-...</code></pre></div>
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+...</code></pre>
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 </div>
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 <div id="i-have-a-matrix-with-too-many-rows-and-i-want-to-simplify-the-row-dendrogram-" class="section level3">
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 <h3 class="hasAnchor">
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 <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>
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 <p>You can first group your rows into several groups and make a group-level dendrogram on it. See following example:</p>
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-<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>)
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+<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>)
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 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))
174 175
 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>)
175 176
 <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), 
176
-    <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>
177
+    <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>
177 178
 <p><img src="most_probably_asked_questions_files/figure-html/unnamed-chunk-6-1.png" width="700"></p>
178 179
 </div>
179 180
 <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
185 186
 <h3 class="hasAnchor">
186 187
 <a href="#how-to-add-axes-for-dendrograms" class="anchor"></a>How to add axes for dendrograms?</h3>
187 188
 <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>
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-<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>)
189
+<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>)
189 190
 
190 191
 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>, 
191 192
     <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
197 198
 })
198 199
 <span class="kw"><a href="../reference/decorate_row_dend.html">decorate_row_dend</a></span>(<span class="st">"foo"</span>, {
199 200
     vp =<span class="st"> </span><span class="kw">current.viewport</span>()
200
-    xscale =<span class="st"> </span>vp<span class="op">$</span>xscale
201
-    <span class="kw">grid.xaxis</span>(<span class="dt">at =</span> xscale[<span class="dv">2</span>] <span class="op">-</span><span class="st"> </span><span class="dv">0</span><span class="op">:</span><span class="dv">5</span>, <span class="dt">label =</span> <span class="dv">0</span><span class="op">:</span><span class="dv">5</span>)
202
-})</code></pre></div>
201
+    xscale =<span class="st"> </span>vp$xscale
202
+    <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>)
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+})</code></pre>
203 204
 <p><img src="most_probably_asked_questions_files/figure-html/unnamed-chunk-7-1.png" width="700"></p>
204 205
 <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>
205 206
 <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>
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@@ -217,19 +218,19 @@ ht =<span class="st"> </span><span class="kw"><a href="../reference/Heatmap.html
217 218
 <h3 class="hasAnchor">
218 219
 <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>
219 220
 <p>You need to assign the dendrograms to a zero-row/column matrix:</p>
220
-<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>)))
221
+<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>)))
221 222
 <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, 
222 223
     <span class="dt">right_annotation =</span> <span class="kw"><a href="../reference/rowAnnotation.html">rowAnnotation</a></span>(
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-        <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>),
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-        <span class="dt">sth =</span> <span class="dv">1</span><span class="op">:</span><span class="dv">10</span>,
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-        <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>)),
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-    <span class="dt">row_split =</span> <span class="dv">2</span>)</code></pre></div>
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+        <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>),
225
+        <span class="dt">sth =</span> <span class="dv">1</span>:<span class="dv">10</span>,
226
+        <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>)),
227
+    <span class="dt">row_split =</span> <span class="dv">2</span>)</code></pre>
227 228
 <p><img src="most_probably_asked_questions_files/figure-html/unnamed-chunk-8-1.png" width="700"></p>
228 229
 </div>
229 230
 <div id="i-still-have-a-problem-with-the-package-and-i-am-lost-in-the-ocean-of-the-huge-vignette-" class="section level3">
230 231
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 <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>
232
-<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>
233
+<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>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">ComplexHeatmap</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">2.1.1</span>
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       </span>
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@@ -84,85 +84,78 @@
84 84
 
85 85
       </header><div class="row">
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   <div class="contents col-md-9">
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+<div id="make-complex-heatmaps" class="section level1">
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+<div class="page-header"><h1 class="hasAnchor">
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+<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>
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+</h1></div>
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-
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-<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>
90 92
 <p><img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="600"></p>
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-<div id="make-complex-heatmaps" class="section level2">
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-<h2 class="hasAnchor">
93
-<a href="#make-complex-heatmaps" class="anchor"></a>Make Complex Heatmaps</h2>
94 93
 <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>
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-<div id="citation" class="section level3">
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-<h3 class="hasAnchor">
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-<a href="#citation" class="anchor"></a>Citation</h3>
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+<div id="citation" class="section level2">
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+<h2 class="hasAnchor">
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+<a href="#citation" class="anchor"></a>Citation</h2>
98 97
 <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>
99 98
 </div>
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-<a href="#documentation" class="anchor"></a>Documentation</h3>
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-<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>
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+<div id="documentation" class="section level2">
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+<h2 class="hasAnchor">
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+<a href="#documentation" class="anchor"></a>Documentation</h2>
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+<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>
104 103
 </div>
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-<div id="install" class="section level3">
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-<h3 class="hasAnchor">
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-<a href="#install" class="anchor"></a>Install</h3>
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+<div id="install" class="section level2">
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+<h2 class="hasAnchor">
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+<a href="#install" class="anchor"></a>Install</h2>
108 107
 <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>
109
-<pre class="{r}"><code>if (!requireNamespace("BiocManager", quietly=TRUE))
110
-    install.packages("BiocManager")
111
-BiocManager::install("ComplexHeatmap")</code></pre>
108
+<p><code>{r} if (!requireNamespace("BiocManager", quietly=TRUE))     install.packages("BiocManager") BiocManager::install("ComplexHeatmap")</code></p>
112 109
 <p>If you want the latest version, install it directly from GitHub:</p>
113
-<pre class="{r}"><code><a href="https://rdrr.io/r/base/library.html">library(devtools)
114
-install_github("jokergoo/ComplexHeatmap")</a></code></pre>
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+<p><code>{r} library(devtools) install_github("jokergoo/ComplexHeatmap")</code></p>
115 111
 </div>
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-<div id="usage" class="section level3">
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-<h3 class="hasAnchor">
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-<a href="#usage" class="anchor"></a>Usage</h3>
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+<div id="usage" class="section level2">
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+<h2 class="hasAnchor">
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+<a href="#usage" class="anchor"></a>Usage</h2>
119 115
 <p>Make a single heatmap:</p>
120
-<pre class="{r}"><code><a href="reference/Heatmap.html">Heatmap(mat, ...)</a></code></pre>
116
+<p><code>{r} Heatmap(mat, ...)</code></p>
121 117
 <p>A single Heatmap with column annotations:</p>
122
-<pre class="{r}"><code>ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...)
123
-Heatmap(mat, ..., top_annotation = ha)</code></pre>
118
+<p><code>{r} ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...) Heatmap(mat, ..., top_annotation = ha)</code></p>
124 119
 <p>Make a list of heatmaps:</p>
125
-<pre class="{r}"><code>Heatmap(mat1, ...) + Heatmap(mat2, ...)</code></pre>
120
+<p><code>{r} Heatmap(mat1, ...) + Heatmap(mat2, ...)</code></p>
126 121
 <p>Make a list of heatmaps and row annotations:</p>
127
-<pre class="{r}"><code>ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row")
128
-Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha</code></pre>
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+<p><code>{r} ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row") Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha</code></p>
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 </div>
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+<div id="examples" class="section level2">
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+<h2 class="hasAnchor">
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+<a href="#examples" class="anchor"></a>Examples</h2>
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+<div id="visualize-methylation-profile-with-complex-annotations" class="section level3">
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 <h3 class="hasAnchor">
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-<a href="#examples" class="anchor"></a>Examples</h3>
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-<a href="#visualize-methylation-profile-with-complex-annotations" class="anchor"></a>Visualize Methylation Profile with Complex Annotations</h4>
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+<a href="#visualize-methylation-profile-with-complex-annotations" class="anchor"></a>Visualize Methylation Profile with Complex Annotations</h3>
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 <p><img src="https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png" alt="complexheatmap_example4"></p>
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 </div>
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-<div id="correlations-between-methylation-expression-and-other-genomic-features" class="section level4">
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-<a href="#correlations-between-methylation-expression-and-other-genomic-features" class="anchor"></a>Correlations between methylation, expression and other genomic features</h4>
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+<div id="correlations-between-methylation-expression-and-other-genomic-features" class="section level3">
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+<h3 class="hasAnchor">
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+<a href="#correlations-between-methylation-expression-and-other-genomic-features" class="anchor"></a>Correlations between methylation, expression and other genomic features</h3>
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 <p><img src="https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png" alt="complexheatmap_example3"></p>
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 </div>
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-<div id="visualize-cell-heterogeneity-from-single-cell-rnaseq" class="section level4">
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-<h4 class="hasAnchor">
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-<a href="#visualize-cell-heterogeneity-from-single-cell-rnaseq" class="anchor"></a>Visualize Cell Heterogeneity from Single Cell RNASeq</h4>
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+<div id="visualize-cell-heterogeneity-from-single-cell-rnaseq" class="section level3">
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+<h3 class="hasAnchor">
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+<a href="#visualize-cell-heterogeneity-from-single-cell-rnaseq" class="anchor"></a>Visualize Cell Heterogeneity from Single Cell RNASeq</h3>
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 <p><img src="https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png" alt="complexheatmap_example2"></p>
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-<a href="#making-enhanced-oncoprint" class="anchor"></a>Making Enhanced OncoPrint</h4>
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+<div id="making-enhanced-oncoprint" class="section level3">
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+<h3 class="hasAnchor">
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+<a href="#making-enhanced-oncoprint" class="anchor"></a>Making Enhanced OncoPrint</h3>
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 <p><img src="https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png" alt="complexheatmap_example1"></p>
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-<a href="#upset-plot" class="anchor"></a>UpSet plot</h4>
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+<div id="upset-plot" class="section level3">
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+<h3 class="hasAnchor">
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+<a href="#upset-plot" class="anchor"></a>UpSet plot</h3>
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+<p><img src="https://pbs.twimg.com/media/Dvpp31uX4AAqGDP.jpg"></p>
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 </div>
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-<div id="license" class="section level3">
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-<a href="#license" class="anchor"></a>License</h3>
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+<div id="license" class="section level2">
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+<h2 class="hasAnchor">
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+<a href="#license" class="anchor"></a>License</h2>
162 156
 <p>MIT @ Zuguang Gu</p>
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 <h2>Dev status</h2>
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-<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>
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+<li><a href="https://travis-ci.org/jokergoo/ComplexHeatmap"><img src="https://travis-ci.org/jokergoo/ComplexHeatmap.svg" alt="Build Status"></a></li>
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+<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>
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+<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>
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+<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>
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+<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>
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 articles:
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>
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     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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 <title>Class for Concatenating Heatmaps and Annotations — AdditiveUnit-class • ComplexHeatmap</title>
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 <!-- jquery -->
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 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../index.html">ComplexHeatmap</a>
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   <a href="https://github.com/jokergoo/ComplexHeatmap">
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     <p>Class for Concatenating Heatmaps and Annotations</p>
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     <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
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 <code><a href='HeatmapAnnotation-class.rd.html'>HeatmapAnnotation-class</a></code> classes. It is only designed for <code>+</code> generic
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 method and the <code>%v%v</code> method so that above three classes can be appended to each other.</p>
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       <td><p>Black hole arguments.</p></td>
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     <p>The heatmap annotation is basically graphics aligned to the heatmap columns or rows.
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 allows subsetting to the annotation to draw a subset of the graphics, which
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 <p>See <code><a href='AnnotationFunction.rd.html'>AnnotationFunction</a></code> constructor for details.</p>
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     <pre class="usage"><span class='fu'><a href='AnnotationFunction.rd.html'>AnnotationFunction</a></span>(<span class='no'>fun</span>, <span class='kw'>fun_name</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>which</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"column"</span>, <span class='st'>"row"</span>),
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     <span class='kw'>var_import</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(), <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>data_scale</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>), <span class='kw'>subset_rule</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(),
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     <span class='kw'>subsetable</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>subset_rule</span>) <span class='kw'>&gt;</span> <span class='fl'>0</span>, <span class='kw'>show_name</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
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       <td><p>The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.</p></td>
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     <p>In the package, we have implemted quite a lot annotation functions by <code><a href='AnnotationFunction.rd.html'>AnnotationFunction</a></code> constructor:
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191 191
 <p>The build-in annotation functions are already enough for most of the analysis, nevertheless, if users
192 192
 want to know more about how to construct the AnnotationFunction class manually, they can refer to
193 193
 <a href='https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#implement-new-annotation-functions.'>https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#implement-new-annotation-functions.</a></p>
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     <p>A <code><a href='AnnotationFunction-class.rd.html'>AnnotationFunction-class</a></code> object which can be used in <code><a href='HeatmapAnnotation.rd.html'>HeatmapAnnotation</a></code>.</p>
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     <h2>Contents</h2>
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8 8
 
9 9
 <title>Class for Color Mapping — ColorMapping-class • ComplexHeatmap</title>
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11
+
11 12
 <!-- jquery -->
12 13
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
13 14
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18 20
 <!-- Font Awesome icons -->
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 </li>
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   <a href="https://github.com/jokergoo/ComplexHeatmap">
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124 126
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     <div class="ref-description">
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     <p>Class for Color Mapping</p>
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     <p>The <code><a href='ColorMapping-class.rd.html'>ColorMapping-class</a></code> handles color mapping for discrete values and continuous values.
136 137
 Discrete values are mapped by setting a vector of colors and continuous values are mapped by setting
137 138
 a color mapping function.</p>
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     <p>The <code><a href='ColorMapping-class.rd.html'>ColorMapping-class</a></code> provides following methods:</p>
... ...
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144 144
 <li><p><code><a href='map_to_colors-ColorMapping-method.rd.html'>map_to_colors,ColorMapping-method</a></code>: mapping values to colors.</p></li>
145 145
 <li><p><code><a href='color_mapping_legend-ColorMapping-method.rd.html'>color_mapping_legend,ColorMapping-method</a></code>: draw legend or get legend as an object.</p></li>
146 146
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179 179
 #&gt; colors:
180 180
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171 171
     <p>This function supports image formats in <code>png</code>, <code>svg</code>, <code>pdf</code>, <code>eps</code>, <code>jpeg/jpg</code>, <code>tiff</code>. 
172 172
 <code>png</code>, <code>jpeg/jpg</code> and <code>tiff</code> images are imported by <code><a href='https://rdrr.io/pkg/png/man/readPNG.html'>readPNG</a></code>, <code><a href='https://rdrr.io/pkg/jpeg/man/readJPEG.html'>readJPEG</a></code> and 
173 173
 <code><a href='https://rdrr.io/pkg/tiff/man/readTIFF.html'>readTIFF</a></code>, and drawn by <code><a href='https://rdrr.io/r/grid/grid.raster.html'>grid.raster</a></code>. <code>svg</code> images are firstly reformatted by <code>rsvg::rsvg_svg</code>
174
-and then imported by <code>readPicture</code> and drawn by <code>grid.picture</code>. <code>pdf</code> and <code>eps</code>
175
-images are imported by <code>PostScriptTrace</code> and <code>readPicture</code>, later drawn by <code>grid.picture</code>.</p>
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+and then imported by <code><a href='https://rdrr.io/pkg/grImport2/man/readPicture.html'>readPicture</a></code> and drawn by <code><a href='https://rdrr.io/pkg/grImport2/man/grid.picture.html'>grid.picture</a></code>. <code>pdf</code> and <code>eps</code>
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+images are imported by <code><a href='https://rdrr.io/pkg/grImport/man/PostScriptTrace.html'>PostScriptTrace</a></code> and <code><a href='https://rdrr.io/pkg/grImport/man/readPicture.html'>readPicture</a></code>, later drawn by <code><a href='https://rdrr.io/pkg/grImport/man/grid.picture.html'>grid.picture</a></code>.</p>
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 <p>Different image formats can be mixed in the <code>image</code> vector.</p>
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184 184
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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     <pre class="examples"><div class='input'><span class='co'># download the free icons from https://github.com/Keyamoon/IcoMoon-Free</span>
186
-<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
187
-<span class='no'>image</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.files.html'>dir</a></span>(<span class='st'>"~/Downloads/IcoMoon-Free-master/PNG/64px"</span>, <span class='kw'>full.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='fl'>10</span>)
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-<span class='no'>anno</span> <span class='kw'>=</span> <span class='fu'>anno_image</span>(<span class='no'>image</span>)
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-<span class='fu'><a href='draw-dispatch.html'>draw</a></span>(<span class='no'>anno</span>, <span class='kw'>test</span> <span class='kw'>=</span> <span class='st'>"png"</span>)
190
-<span class='no'>image</span>[<span class='fl'>1</span>:<span class='fl'>5</span>] <span class='kw'>=</span> <span class='st'>""</span>
191
-<span class='no'>anno</span> <span class='kw'>=</span> <span class='fu'>anno_image</span>(<span class='no'>image</span>)
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-<span class='fu'><a href='draw-dispatch.html'>draw</a></span>(<span class='no'>anno</span>, <span class='kw'>test</span> <span class='kw'>=</span> <span class='st'>"some of png"</span>)
193
-}</div></pre>
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+<span class='co'># \dontrun{</span>
187
+<span class='no'>image</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.files.html'>dir</a></span>(<span class='st'>"~/Downloads/IcoMoon-Free-master/PNG/64px"</span>, <span class='kw'>full.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='fl'>10</span>)</div><div class='output co'>#&gt; <span class='error'>Error in sample.int(length(x), size, replace, prob): invalid first argument</span></div><div class='input'><span class='no'>anno</span> <span class='kw'>=</span> <span class='fu'>anno_image</span>(<span class='no'>image</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: is.na() applied to non-(list or vector) of type 'closure'</span></div><div class='output co'>#&gt; <span class='error'>Error in image[is.na(image)] &lt;- "": object of type 'closure' is not subsettable</span></div><div class='input'><span class='fu'><a href='draw-dispatch.html'>draw</a></span>(<span class='no'>anno</span>, <span class='kw'>test</span> <span class='kw'>=</span> <span class='st'>"png"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in draw(anno, test = "png"): object 'anno' not found</span></div><div class='input'><span class='no'>image</span>[<span class='fl'>1</span>:<span class='fl'>5</span>] <span class='kw'>=</span> <span class='st'>""</span></div><div class='output co'>#&gt; <span class='error'>Error in image[1:5] = "": object of type 'closure' is not subsettable</span></div><div class='input'><span class='no'>anno</span> <span class='kw'>=</span> <span class='fu'>anno_image</span>(<span class='no'>image</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: is.na() applied to non-(list or vector) of type 'closure'</span></div><div class='output co'>#&gt; <span class='error'>Error in image[is.na(image)] &lt;- "": object of type 'closure' is not subsettable</span></div><div class='input'><span class='fu'><a href='draw-dispatch.html'>draw</a></span>(<span class='no'>anno</span>, <span class='kw'>test</span> <span class='kw'>=</span> <span class='st'>"some of png"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in draw(anno, test = "some of png"): object 'anno' not found</span></div><div class='input'># }
188
+</div></pre>
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