Description Usage Arguments Details Value Author(s) References See Also
View source: R/cutreeWrapper.R
This wrapper provides a common access point for two methods of adaptive branch pruning of hierarchical clustering dendrograms.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27  cutreeDynamic(
dendro, cutHeight = NULL, minClusterSize = 20,
# Basic tree cut options
method = "hybrid", distM = NULL,
deepSplit = (ifelse(method=="hybrid", 1, FALSE)),
# 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, maxDistToLabel = NULL,
maxPamDist = cutHeight,
respectSmallClusters = TRUE,
# Various options
verbose = 2, indent = 0)

dendro 
A hierarchical clustering dendorgram such as one returned by 
cutHeight 
Maximum joining heights that will be considered. For 
minClusterSize 
Minimum cluster size. 
method 
Chooses the method to use. Recognized values are "hybrid" and "tree". 
distM 
Only used for method "hybrid". The distance matrix used as input to 
deepSplit 
For method "hybrid", can be either logical or integer in the range 0 to 4. For method
"tree", must be logical. In both cases, provides a rough control over sensitivity to cluster splitting.
The higher the value (or if 
maxCoreScatter 
Only used for method "hybrid".
Maximum scatter of the core for a branch to be a cluster, given as the fraction of 
minGap 
Only used for method "hybrid".
Minimum cluster gap given as the fraction of the difference between 
maxAbsCoreScatter 
Only used for method "hybrid".
Maximum scatter of the core for a branch to be a cluster given as absolute heights. If given, overrides

minAbsGap 
Only used for method "hybrid".
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 
Only used for method "hybrid". If TRUE, the second (PAMlike) stage will be performed. 
pamRespectsDendro 
Logical, only used for method "hybrid". If 
useMedoids 
Only used for method "hybrid" and only if 
maxDistToLabel 
Deprecated, use 
maxPamDist 
Only used for method "hybrid" and only if 
respectSmallClusters 
Only used for method "hybrid" and only if 
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 
This is a wrapper for two related but different methods for cluster detection in hierarchical clustering dendrograms.
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 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.
Peter Langfelder, Peter.Langfelder@gmail.com
Langfelder P, Zhang B, Horvath S, 2007. http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting
hclust
, cutreeHybrid
, cutreeDynamicTree
.
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