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 (user-supplied) 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 (PAM-like) 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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