cutreedynamic

距离变换的实现方案及代码

cutreeDynamic         package:dynamicTreeCut         R Documentation

_A_d_a_p_t_i_v_e _b_r_a_n_c_h _p_r_u_n_i_n_g _o_f _h_i_e_r_a_r_c_h_i_c_a_l _c_l_u_s_t_e_r_i_n_g _d_e_n_d_r_o_g_r_a_m_s.

_D_e_s_c_r_i_p_t_i_o_n:

     This wrapper provides a common access point for two methods of
     adaptive branch pruning of hierarchical clustering dendrograms.

_U_s_a_g_e:

     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)

_A_r_g_u_m_e_n_t_s:

  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 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 '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'.  

clusterTrim: Only used for method "hybrid".  Specifies the fraction of
          the cluster height that will be trimmed before stage 2; all
          objects joining above the '1-ClusterTrim' fraction of the
          cluster height will be trimmed. If set to 0 or less, nothing
          will be trimmed. 

labelUnlabeled: Only used for method "hybrid".  if TRUE, the second
          (PAM-like) stage will be performed.  

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. 

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

     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.

_A_u_t_h_o_r(_s):

     Peter Langfelder, [e-mail]

_R_e_f_e_r_e_n_c_e_s:

     Langfelder P, Zhang B, Horvath S, 2007. <URL:
     http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting>

_S_e_e _A_l_s_o:

     'hclust', 'cutreeHybrid', 'cutreeDynamicTree'.