cutreehybrid

距离变换的实现方案及代码

cutreeHybrid         package:dynamicTreeCut         R Documentation

_H_y_b_r_i_d _a_d_a_p_t_i_v_e _t_r_e_e _c_u_t _f_o_r _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:

     Detect clusters in a dendorgram produced by the function 'hclust'.

_U_s_a_g_e:

     cutreeHybrid(dendro, distM, cutHeight = NULL, minClusterSize = 20, 
                  deepSplit = 1,
                  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'.  

   distM: Distance matrix that was used as input to 'hclust'.  

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 3. 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' and 'minGap' below.

maxCoreScatter: 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: Minimum cluster gap given as the fraction of the difference
          between 'cutHeight' and the 5th percentile of joining
          heights.  

maxAbsCoreScatter: Maximum scatter of the core for a branch to be a
          cluster given as absolute heights. If given, overrides
          'maxCoreScatter'.  

minAbsGap: Minimum cluster gap given as absolute height difference. If
          given, overrides 'minGap'.  

clusterTrim: 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: If TRUE, the second (PAM-like) stage will be performed.            

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. 

maxDistToLabel: Maximum object distance to closest cluster that will
          result in the object assigned to that cluster.  

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 '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:

     The function detects clusters in a hierarchical dendrogram based
     on the shape of branches on the dendrogram. For details on the
     method, see <URL:
     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.

_V_a_l_u_e:

     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.

 trimmed: Numerical labels indicating objects that have been trimmed
          from clusters.  

branches: A list detailing the deteced branch structure.  

_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', 'as.dist'