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README.html
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README.html
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<div id="content">
<h1 class="title">birch-beer</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgb2401ab">Description</a></li>
<li><a href="#org13e194b">Installation</a>
<ul>
<li><a href="#orgb46a304">Use <code>nix</code></a></li>
<li><a href="#org204682d">Dependencies</a></li>
<li><a href="#org130b38e">Install <code>stack</code></a></li>
<li><a href="#org69ff251">Install <code>birch-beer</code></a>
<ul>
<li><a href="#org69b0f3c">Source</a></li>
<li><a href="#orgd99969a">Online</a></li>
<li><a href="#org07fbfab">Docker</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org7da20b4">Usage</a>
<ul>
<li><a href="#org20af828">Tree format</a>
<ul>
<li><a href="#org471f2dc">Example conversion from R</a></li>
</ul>
</li>
<li><a href="#orgf00c8d8">Labels format</a></li>
</ul>
</li>
<li><a href="#org56730ad">Select examples</a>
<ul>
<li><a href="#org138221b">Large tree</a></li>
<li><a href="#org4c2efa2">Number overlay</a></li>
<li><a href="#org7b1494c">Distance overlay</a></li>
<li><a href="#org0d7221d">Continuous color saturation</a></li>
<li><a href="#orgb7a229c">Continuous multi-color saturation</a></li>
<li><a href="#org51ecb12">Diversity of labels</a></li>
</ul>
</li>
</ul>
</div>
</div>
<p>
<a href="https://gregoryschwartz.github.io/birch-beer/">Website</a>
</p>
<p>
See <a href="https://github.com/GregorySchwartz/birch-beer">https://github.com/GregorySchwartz/birch-beer</a> for latest version.
</p>
<div id="outline-container-orgb2401ab" class="outline-2">
<h2 id="orgb2401ab">Description</h2>
<div class="outline-text-2" id="text-orgb2401ab">
<div id="orgacb21bd" class="figure">
<p><img src="img/piechart_pruned_tree.png" alt="piechart_pruned_tree.png" />
</p>
</div>
<p>
<code>birch-beer</code> is all about sweet trees. That is, visualizing hierarchical
structures where the elements are stored in leaves and parent nodes represent
all of the descendant leaves. Using branch scaling, weighted average color
blending, distance markers, and more, we can all create some home brewed
<code>birch-beer</code> together!
</p>
</div>
</div>
<div id="outline-container-org13e194b" class="outline-2">
<h2 id="org13e194b">Installation</h2>
<div class="outline-text-2" id="text-org13e194b">
</div>
<div id="outline-container-orgb46a304" class="outline-3">
<h3 id="orgb46a304">Use <code>nix</code></h3>
<div class="outline-text-3" id="text-orgb46a304">
<p>
Installing <code>birch-beer</code> using <code>nix</code> is the easiest way to install from source.
First, install <code>nix</code> following the instructions
<a href="https://nixos.org/nix/">on the website</a>. Then run the commands:
</p>
<div class="org-src-container">
<pre class="src src-sh">git clone https://github.com/GregorySchwartz/birch-beer.git
<span style="color: #ff8700;">cd</span> birch-beer
nix-env -f default.nix -i birch-beer
</pre>
</div>
<p>
Then the <code>birch-beer</code> command should be in your path! If you do not wish to use
<code>nix</code> or <code>docker</code>, then you can continue reading for dependencies and <code>stack</code>
installation (no longer supported).
</p>
</div>
</div>
<div id="outline-container-org204682d" class="outline-3">
<h3 id="org204682d">Dependencies</h3>
<div class="outline-text-3" id="text-org204682d">
<p>
You may require the following dependencies to build and run (from Ubuntu 16.04,
use the appropriate packages from your distribution of choice):
</p>
<ul class="org-ul">
<li>build-essential</li>
<li>libgmp-dev</li>
<li>libblas-dev</li>
<li>liblapack-dev</li>
<li>libgsl-dev</li>
<li>libgtk2.0-dev</li>
<li>libcairo2-dev</li>
<li>libpango1.0-dev</li>
<li>graphviz</li>
</ul>
</div>
</div>
<div id="outline-container-org130b38e" class="outline-3">
<h3 id="org130b38e">Install <code>stack</code></h3>
<div class="outline-text-3" id="text-org130b38e">
<p>
See <a href="https://docs.haskellstack.org/en/stable/README/">https://docs.haskellstack.org/en/stable/README/</a> for more details.
</p>
<div class="org-src-container">
<pre class="src src-sh">curl -sSL https://get.haskellstack.org/ | sh
stack setup
</pre>
</div>
</div>
</div>
<div id="outline-container-org69ff251" class="outline-3">
<h3 id="org69ff251">Install <code>birch-beer</code></h3>
<div class="outline-text-3" id="text-org69ff251">
</div>
<div id="outline-container-org69b0f3c" class="outline-4">
<h4 id="org69b0f3c">Source</h4>
<div class="outline-text-4" id="text-org69b0f3c">
<p>
Probably the easiest method if you don't want to mess with dependencies (outside
of the ones above).
</p>
<div class="org-src-container">
<pre class="src src-sh">git clone https://github.com/GregorySchwartz/birch-beer.git
<span style="color: #ff8700;">cd</span> birch-beer
stack install
</pre>
</div>
</div>
</div>
<div id="outline-container-orgd99969a" class="outline-4">
<h4 id="orgd99969a">Online</h4>
<div class="outline-text-4" id="text-orgd99969a">
<p>
We only require <code>stack</code> (or <code>cabal</code>), you do not need to download any source
code (but you might need the stack.yaml dependency versions), just run the
following command to place <code>birch-beer</code> in your <code>~/.local/bin/</code>:
</p>
<div class="org-src-container">
<pre class="src src-sh">stack install birch-beer
</pre>
</div>
<p>
If you run into errors like <code>Error: While constructing the build plan, the
following exceptions were encountered:</code>, then follow it's advice. Usually you
just need to follow the suggestion and add the dependencies to the specified
file. For a quick <code>yaml</code> configuration, refer to
<a href="https://github.com/GregorySchwartz/birch-beer/blob/master/stack.yaml">https://github.com/GregorySchwartz/birch-beer/blob/master/stack.yaml</a>. Relies on
<code>eigen-3.3.4.1</code> right now.
</p>
</div>
</div>
<div id="outline-container-org07fbfab" class="outline-4">
<h4 id="org07fbfab">Docker</h4>
<div class="outline-text-4" id="text-org07fbfab">
<p>
Different computers have different setups, operating systems, and repositories.
Do put the entire program in a container to bypass difficulties (with the other
methods above), we user <code>docker</code>. So first, <a href="https://docs.docker.com/">install docker</a>.
</p>
<p>
To get <code>birch-beer</code> (replace 0.1.0.0 with <a href="https://cloud.docker.com/repository/docker/gregoryschwartz/birch-beer/general">any version needed</a>):
</p>
<div class="org-src-container">
<pre class="src src-sh">docker pull gregoryschwartz/birch-beer:0.1.0.0
</pre>
</div>
<p>
To run <code>birch-beer</code> in a docker container:
</p>
<div class="org-src-container">
<pre class="src src-sh">sudo docker run gregoryschwartz/birch-beer:0.1.0.0 -h
</pre>
</div>
<p>
To build the <code>birch-beer</code> image yourself if you want:
</p>
<div class="org-src-container">
<pre class="src src-sh">git clone https://github.com/GregorySchwartz/birch-beer.git
<span style="color: #ff8700;">cd</span> birch-beer
docker build -t birch-beer -f ./Dockerfile .
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="outline-container-org7da20b4" class="outline-2">
<h2 id="org7da20b4">Usage</h2>
<div class="outline-text-2" id="text-org7da20b4">
<p>
<b>For a more detailed look at many of the features</b>, check out the
<code>too-many-cells</code> <a href="https://github.com/GregorySchwartz/too-many-cells">README</a> about <code>make-tree</code>, which uses <code>birch-beer</code> to plot
single cell clades with examples. At any point, use <code>birch-beer -h</code> to see the
help. The general usage would be:
</p>
<div class="org-src-container">
<pre class="src src-bash">birch-beer --input tree.json --labels-file labels.csv
</pre>
</div>
</div>
<div id="outline-container-org20af828" class="outline-3">
<h3 id="org20af828">Tree format</h3>
<div class="outline-text-3" id="text-org20af828">
<p>
The input tree format should be a <code>json</code> file with a recursive structure. An
object is represented by <code>[{"_distance": DOUBLE, "_item": [STRING]},
[SUBFOREST]]</code>, where <code>"_distance"</code> and <code>"_item"</code> are optional (otherwise use
<code>{}</code>), having <code>"_distance"</code> for inner nodes and <code>"_item"</code> for leaves. Supports
rose trees as well! For example:
</p>
<pre class="example" id="orga79e267">
[{"_distance": 0.8}, [[{"_item": ["1", "2"]}, [[{"_item": ["3", "4", "5"]}, []], [{"_item": ["6", "7"]}, []]]], [{"_item": ["8", "9", "10", "11"]}, []]]]
</pre>
</div>
<div id="outline-container-org471f2dc" class="outline-4">
<h4 id="org471f2dc">Example conversion from R</h4>
<div class="outline-text-4" id="text-org471f2dc">
<p>
To get to the required format, here is an example to get from an R <code>hclust</code> tree
to the appropriate <code>json</code>.
</p>
<div class="org-src-container">
<pre class="src src-R"><span style="color: #d787af;">library</span><span style="color: #008787;">(</span>dendextend<span style="color: #008787;">)</span>
<span style="color: #d787af;">library</span><span style="color: #008787;">(</span>data.tree<span style="color: #008787;">)</span>
<span style="color: #d787af;">library</span><span style="color: #008787;">(</span>jsonlite<span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Get hclust tree.</span>
hc = hclust<span style="color: #008787;">(</span>dist<span style="color: #d75f87;">(</span>USArrests<span style="color: #d75f87;">)</span>, <span style="color: #afaf00;">"ave"</span><span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Get dendrogram.</span>
dend = as.dendrogram<span style="color: #008787;">(</span>hc<span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Get nicely formatted tree from dendrogram.</span>
tree = as.Node<span style="color: #008787;">(</span>dend<span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Convert to JSON</span>
json = toJSON<span style="color: #008787;">(</span>as.list<span style="color: #d75f87;">(</span>tree, mode = <span style="color: #afaf00;">"explicit"</span>, unname = <span style="color: #d787af;">TRUE</span><span style="color: #d75f87;">)</span><span style="color: #008787;">)</span>
<span style="color: #767676;"># </span><span style="color: #767676;">Write to file</span>
cat<span style="color: #008787;">(</span>json, file = <span style="color: #afaf00;">"tree.json"</span><span style="color: #008787;">)</span>
</pre>
</div>
<p>
Saving this file as <code>tree.json</code>, we continue to format as such (this could be a
single command, but was split to make clearer). Here, we use
<a href="https://stedolan.github.io/jq/"> <code>jq</code> </a>, the command line <code>json</code> processor.
</p>
<div class="org-src-container">
<pre class="src src-bash">cat tree.json <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf") | not) then del(.name) else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then del(.members) | del(.midpoint) | del(.value) | del(.plotHeight) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf")) then ._item = .name | del(.name) else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf") | not) then [{}, [.children[]]] else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
| jq -c <span style="color: #afaf00;">'walk( if (type == "object") then (if (has("leaf")) then [{_item}, []] else . end) else . end)'</span> <span style="color: #afaf00;">\</span>
> formatted_tree.json
</pre>
</div>
<p>
Then we can see the tree using birch-beer.
</p>
<div class="org-src-container">
<pre class="src src-bash">birch-beer -i formatted_tree.json
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-orgf00c8d8" class="outline-3">
<h3 id="orgf00c8d8">Labels format</h3>
<div class="outline-text-3" id="text-orgf00c8d8">
<p>
To assign labels (and thus colors) to the elements within the tree, make a <code>csv</code>
file with an <code>item,label</code> format. Both columns are treated as strings, so
anything can be used as long as the <code>item</code> column matches the item strings in
the tree. For example to go with the above tree:
</p>
<pre class="example" id="org7f7bf40">
item,label
1,1
2,1
3,2
4,2
5,2
6,3
7,1
8,1
9,3
10,3
11,2
</pre>
</div>
</div>
</div>
<div id="outline-container-org56730ad" class="outline-2">
<h2 id="org56730ad">Select examples</h2>
<div class="outline-text-2" id="text-org56730ad">
</div>
<div id="outline-container-org138221b" class="outline-3">
<h3 id="org138221b">Large tree</h3>
<div class="outline-text-3" id="text-org138221b">
<div id="orgc1bb30b" class="figure">
<p><img src="img/complete_default_tree.png" alt="complete_default_tree.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org4c2efa2" class="outline-3">
<h3 id="org4c2efa2">Number overlay</h3>
<div class="outline-text-3" id="text-org4c2efa2">
<div id="orgeb17f84" class="figure">
<p><img src="img/numbered_pruned_tree.png" alt="numbered_pruned_tree.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org7b1494c" class="outline-3">
<h3 id="org7b1494c">Distance overlay</h3>
<div class="outline-text-3" id="text-org7b1494c">
<div id="org1f83293" class="figure">
<p><img src="img/modularity_pruned_tree.png" alt="modularity_pruned_tree.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org0d7221d" class="outline-3">
<h3 id="org0d7221d">Continuous color saturation</h3>
<div class="outline-text-3" id="text-org0d7221d">
<div id="orgff8e284" class="figure">
<p><img src="img/cd4_saturated_10_dendrogram.png" alt="cd4_saturated_10_dendrogram.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-orgb7a229c" class="outline-3">
<h3 id="orgb7a229c">Continuous multi-color saturation</h3>
<div class="outline-text-3" id="text-orgb7a229c">
<div id="org9e1f052" class="figure">
<p><img src="img/cd4_cd8_sat_10_dendrogram.png" alt="cd4_cd8_sat_10_dendrogram.png" />
</p>
</div>
</div>
</div>
<div id="outline-container-org51ecb12" class="outline-3">
<h3 id="org51ecb12">Diversity of labels</h3>
<div class="outline-text-3" id="text-org51ecb12">
<div id="org01f5ba3" class="figure">
<p><img src="img/diversity_pruned_tree.png" alt="diversity_pruned_tree.png" />
</p>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Gregory W. Schwartz</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>