cutreeDynamic {dynamicTreeCut} | R Documentation |
This wrapper provides a common access point for two methods of adaptive branch pruning of hierarchical clustering dendrograms.
cutreeDynamic(dendro, cutHeight = NULL, minClusterSize = 20, method = "hybrid", distM = NULL, deepSplit = (ifelse(method=="hybrid", 1, FALSE)), maxCoreScatter = NULL, minGap = NULL, maxAbsCoreScatter = NULL, minAbsGap = NULL, pamStage = TRUE, pamRespectsDendro = TRUE, useMedoids = FALSE, maxDistToLabel = cutHeight, respectSmallClusters = TRUE, verbose = 2, indent = 0)
dendro |
A hierarchical clustering dendorgram such as one returned by hclust . |
cutHeight |
Maximum joining heights that will be considered. For method=="tree" it
defaults to 0.99. For method=="hybrid" it defaults to 99
percentile and the maximum of the joining heights on the dendrogram. |
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 hclust . If not
given and method == "hybrid" , the function will issue a warning and default to method =
"tree" . |
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 TRUE ), the more and smaller clusters will be produced. For the
"hybrid" method, a finer control can be achieved via maxCoreScatter and minGap below. |
maxCoreScatter |
Only used for method "hybrid".
Maximum scatter of the core for a branch to be a cluster, given as the fraction of cutHeight
relative to the 5th percentile of joining heights. See Details. |
minGap |
Only used for method "hybrid".
Minimum cluster gap given as the fraction of the difference between cutHeight and the 5th
percentile of joining heights. |
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
maxCoreScatter . |
minAbsGap |
Only used for method "hybrid".
Minimum cluster gap given as absolute height difference. If given, overrides minGap . |
pamStage |
Only used for method "hybrid". If TRUE, the second (PAM-like) stage will be performed. |
pamRespectsDendro |
Logical, only used for method "hybrid". If TRUE , the PAM stage will
respect the dendrogram in the sense that objects and small clusters will only be assigned to clusters
that belong to the same branch that the objects or small clusters being assigned belong to.
|
useMedoids |
Only used for method "hybrid" and only if labelUnlabeled==TRUE .
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. |
maxDistToLabel |
Only used for method "hybrid" and only if labelUnlabeled==TRUE .
Maximum object distance to closest cluster that will result in the object
assigned to that cluster. |
respectSmallClusters |
Only used for method "hybrid" and only if labelUnlabeled==TRUE .
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 verbose above). Each unit
adds two spaces before printed messages; useful when several functions' output is to be nested. |
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
.