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<table width="100%" summary="page for cutreeDynamic {dynamicTreeCut}"><tr><td>cutreeDynamic {dynamicTreeCut}</td><td align="right">R Documentation</td></tr></table>
<h2>Adaptive branch pruning of hierarchical clustering dendrograms.</h2>
<h3>Description</h3>
<p>
This wrapper provides a common access point for two methods of adaptive branch pruning of hierarchical
clustering dendrograms.
</p>
<h3>Usage</h3>
<pre>
cutreeDynamic(dendro, cutHeight = NULL, minClusterSize = 20, method = "hybrid",
distM = NULL,
deepSplit = (ifelse(method=="hybrid", 1, FALSE)),
maxCoreScatter = NULL, minGap = NULL,
maxAbsCoreScatter = NULL, minAbsGap = NULL, clusterTrim = 0,
labelUnlabeled = TRUE,
useMedoids = FALSE, maxDistToLabel = cutHeight,
respectSmallClusters = TRUE,
verbose = 2, indent = 0)
</pre>
<h3>Arguments</h3>
<table summary="R argblock">
<tr valign="top"><td><code>dendro</code></td>
<td>
A hierarchical clustering dendorgram such as one returned by <code>hclust</code>. </td></tr>
<tr valign="top"><td><code>cutHeight</code></td>
<td>
Maximum joining heights that will be considered. For <code>method=="tree"</code> it
defaults to 0.99. For <code>method=="hybrid"</code> it defaults to 99
percentile and the maximum of the joining heights on the dendrogram.</td></tr>
<tr valign="top"><td><code>minClusterSize</code></td>
<td>
Minimum cluster size. </td></tr>
<tr valign="top"><td><code>method</code></td>
<td>
Chooses the method to use. Recognized values are "hybrid" and "tree". </td></tr>
<tr valign="top"><td><code>distM</code></td>
<td>
Only used for method "hybrid". The distance matrix used as input to <code>hclust</code>. If not
given and <code>method == "hybrid"</code>, the function will issue a warning and default to <code>method =
"tree"</code>.</td></tr>
<tr valign="top"><td><code>deepSplit</code></td>
<td>
For method "hybrid", can be either logical or integer in the range 0 to 3. For method
"tree", must be logical. In both cases, provides a rough control over sensitivity to cluster splitting.
The higher the value (or if <code>TRUE</code>), the more and smaller clusters will be produced. For the
"hybrid" method, a finer control can be achieved via <code>maxCoreScatter</code> and <code>minGap</code> below.</td></tr>
<tr valign="top"><td><code>maxCoreScatter</code></td>
<td>
Only used for method "hybrid".
Maximum scatter of the core for a branch to be a cluster, given as the fraction of <code>cutHeight</code>
relative to the 5th percentile of joining heights. See Details. </td></tr>
<tr valign="top"><td><code>minGap</code></td>
<td>
Only used for method "hybrid".
Minimum cluster gap given as the fraction of the difference between <code>cutHeight</code> and the 5th
percentile of joining heights. </td></tr>
<tr valign="top"><td><code>maxAbsCoreScatter</code></td>
<td>
Only used for method "hybrid".
Maximum scatter of the core for a branch to be a cluster given as absolute heights. If given, overrides
<code>maxCoreScatter</code>. </td></tr>
<tr valign="top"><td><code>minAbsGap</code></td>
<td>
Only used for method "hybrid".
Minimum cluster gap given as absolute height difference. If given, overrides <code>minGap</code>. </td></tr>
<tr valign="top"><td><code>clusterTrim</code></td>
<td>
Only used for method "hybrid".
Specifies the fraction of the cluster height that will be trimmed before stage
2; all objects joining above the <code>1-ClusterTrim</code> fraction of the cluster height will be trimmed.
If set to 0 or less, nothing will be trimmed. </td></tr>
<tr valign="top"><td><code>labelUnlabeled</code></td>
<td>
Only used for method "hybrid".
if TRUE, the second (PAM-like) stage will be performed. </td></tr>
<tr valign="top"><td><code>useMedoids</code></td>
<td>
Only used for method "hybrid" and only if <code>labelUnlabeled==TRUE</code>.
If TRUE, the second stage will be use object to medoid distance; if FALSE, it
will use average object to cluster distance. The default (FALSE) is recommended. </td></tr>
<tr valign="top"><td><code>maxDistToLabel</code></td>
<td>
Only used for method "hybrid" and only if <code>labelUnlabeled==TRUE</code>.
Maximum object distance to closest cluster that will result in the object
assigned to that cluster. </td></tr>
<tr valign="top"><td><code>respectSmallClusters</code></td>
<td>
Only used for method "hybrid" and only if <code>labelUnlabeled==TRUE</code>.
If TRUE, branches that failed to be clusters in stage 1 only because of
insufficient size will be assigned together in stage 2. If FALSE, all objects will be assigned
individually.</td></tr>
<tr valign="top"><td><code>verbose</code></td>
<td>
Controls the verbosity of the output. 0 will make the function completely quiet,
values up to 4 gradually increase verbosity.</td></tr>
<tr valign="top"><td><code>indent</code></td>
<td>
Controls indentation of printed messages (see <code>verbose</code> above). Each unit
adds two spaces before printed messages; useful when several functions' output is to be nested. </td></tr>
</table>
<h3>Details</h3>
<p>
This is a wrapper for two related but different methods for cluster detection in hierarchical
clustering dendrograms.
</p>
<p>
In order to make the shape parameters <code>maxCoreScatter</code> and <code>minGap</code> more universal, their
values are interpreted relative to <code>cutHeight</code> and the 5th percetile of the merging heights (we
arbitrarily chose the 5th percetile rather than the minimum for reasons of stability). Thus, the absolute
maximum allowable core scatter is calculated as <code>maxCoreScatter * (cutHeight - refHeight) +
refHeight</code> and the absolute minimum allowable gap as <code>minGap * (cutHeight - refHeight)</code>, where
<code>refHeight</code> is the 5th percentile of the merging heights.
</p>
<h3>Value</h3>
<p>
A vector of numerical labels giving assignment of objects to modules. Unassigned objects are labeled
0, the largest module has label 1, next largest 2 etc.</p>
<h3>Author(s)</h3>
<p>
Peter Langfelder, <a href="mailto:Peter.Langfelder@gmail.com">Peter.Langfelder@gmail.com</a>
</p>
<h3>References</h3>
<p>
Langfelder P, Zhang B, Horvath S, 2007.
<a href="http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting">http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting</a>
</p>
<h3>See Also</h3>
<p>
<code><a href="../../stats/html/hclust.html">hclust</a></code>, <code><a href="cutreeHybrid.html">cutreeHybrid</a></code>, <code><a href="cutreeDynamicTree.html">cutreeDynamicTree</a></code>.
</p>
<hr><div align="center">[Package <em>dynamicTreeCut</em> version 1.11-3 <a href="00Index.html">Index]</a></div>
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