cutreeHybrid {dynamicTreeCut}  R Documentation 
Detect clusters in a dendorgram produced by the function hclust
.
cutreeHybrid( # Input data: basic tree cutiing dendro, distM, # Branch cut criteria and options cutHeight = NULL, minClusterSize = 20, deepSplit = 1, # Advanced options maxCoreScatter = NULL, minGap = NULL, maxAbsCoreScatter = NULL, minAbsGap = NULL, minSplitHeight = NULL, minAbsSplitHeight = NULL, # External (usersupplied) measure of branch split externalBranchSplitFnc = NULL, minExternalSplit = NULL, externalSplitOptions = list(), externalSplitFncNeedsDistance = NULL, assumeSimpleExternalSpecification = TRUE, # PAM stage options pamStage = TRUE, pamRespectsDendro = TRUE, useMedoids = FALSE, maxPamDist = cutHeight, respectSmallClusters = TRUE, # Various options verbose = 2, indent = 0)
dendro 
a hierarchical clustering dendorgram such as one returned by 
distM 
Distance matrix that was used as input to 
cutHeight 
Maximum joining heights that will be considered. It defaults to 99 of the range between the 5th percentile and the maximum of the joining heights on the dendrogram. 
minClusterSize 
Minimum cluster size. 
deepSplit 
Either logical or integer in the range 0 to 4. Provides a rough control over
sensitivity to cluster splitting. The higher the value, the more and smaller clusters will be produced.
A finer control can be achieved via 
maxCoreScatter 
Maximum scatter of the core for a branch to be a cluster, given as the fraction
of 
minGap 
Minimum cluster gap given as the fraction of the difference between 
maxAbsCoreScatter 
Maximum scatter of the core for a branch to be a cluster given as absolute
heights. If given, overrides 
minAbsGap 
Minimum cluster gap given as absolute height difference. If given, overrides

minSplitHeight 
Minimum split height given as the fraction of the difference between

minAbsSplitHeight 
Minimum split height given as an absolute height.
Branches merging below this height will automatically be merged. If not given (default), will be determined
from 
externalBranchSplitFnc 
Optional function to evaluate split (dissimilarity) between two branches.
Either a single function or a list in which each component is a function (see

minExternalSplit 
Thresholds to decide whether two branches should be merged.
It should be a numeric vector of the same length as the number of functions in

externalSplitOptions 
Further arguments to function 
externalSplitFncNeedsDistance 
Optional specification of whether the external branch split
functions need the distance matrix as one of their arguments. Either 
assumeSimpleExternalSpecification 
Logical: when 
pamStage 
Logical, only used for method "hybrid". If 
pamRespectsDendro 
Logical, only used for method "hybrid".
If 
useMedoids 
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. 
maxPamDist 
Maximum object distance to closest cluster that will result in the object
assigned to that cluster. Defaults to 
respectSmallClusters 
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. 
verbose 
Controls the verbosity of the output. 0 will make the function completely quiet, values up to 4 gradually increase verbosity. 
indent 
Controls indentation of printed messages (see 
The function detects clusters in a hierarchical dendrogram based on the shape of branches on the dendrogram. For details on the method, see http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting.
In order to make the shape parameters maxCoreScatter
and minGap
more universal, their
values are interpreted relative to cutHeight
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 maxCoreScatter * (cutHeight  refHeight) +
refHeight
and the absolute minimum allowable gap as minGap * (cutHeight  refHeight)
, where
refHeight
is the 5th percentile of the merging heights.
A list containg the following elements:
labels 
Numerical labels of clusters, with 0 meaning unassigned, label 1 labeling the largest cluster etc. 
cores 
Numerical labels indicating cores of found clusters. 
smallLabels 
Numerical labels for branches that failed to be recognized clusters only because of insufficient number of objects. 
mergeDiagnostics 
A data.frame with one row per merge in the input dendrogram. The columns give the values of the various merging criteria used by the algorithm. Missing data indicate that at least one of the "branches" merged was actually a singleton (single node) and hence the branch merging was automatic. 
mergeCriteria 
Values of the merging thresholds. Either a copy of the corresponding input thresholds
or values determined by 
branches 
A list detailing the deteced branch structure. 
Peter Langfelder, Peter.Langfelder@gmail.com
Langfelder P, Zhang B, Horvath S, 2007. http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting