clusterVisualHclust-class     package:goCluster     R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     This class can be used in order to visualize annotation terms that
     have been found as overrepresented in clusters identified with a
     hierarchical clustering. These annotation terms are displayed
     alongside the hierarchical clustering result.

_D_e_t_a_i_l_s:

     The class provides a wrapper around the 'prepareAxis'-function.
     Please read the corresponding documentation for further details.

_S_l_o_t_s:

     '_p_r_e_p_a_r_e_d': Object of class '"list"', the number of vectors stored
          in this list corresponds to the number of annotations
          analyzed. Each vector contains the same number of items as
          there are nodes in the tree of the clustering (number of
          genes - 1). The order of appearence corresponds to the
          ordering of the dendrogram so that the sorted dendrogram and
          the annotation terms can be put alongside each other.

          Additional slots are described in the documentation of the
          'clusterVisual-class' and 'clusterModule-class'.

_E_x_t_e_n_d_s:

     Class '"clusterVisual"', directly. Class '"clusterModule"', by
     class '"clusterVisual"'.

_M_e_t_h_o_d_s:

     _c_o_n_f_i_g 'signature(object = "clusterVisualHclust")': interactive
          setup of the class. There are no options that you can set on
          this class.

     _s_e_t_u_p 'signature(object = "clusterVisualHclust")': returns the
          configuration of the object as a list. Since there are no
          options to this class, this is always an empty list. 

     _s_e_t_u_p<- 'signature(object = "clusterVisualHclust")':
          non-interactive setup of the class. Not necessary since this
          class has no options.

     _e_x_e_c_u_t_e 'signature(object = "clusterVisualHclust")': prepares the
          selected annotation terms for the visualization. 

     _r_e_s_e_t 'signature(object = "clusterVisualHclust")': resets the
          results of this class so that the analysis can be run again. 

     _d_i_s_p_l_a_y 'signature(object = "clusterVisualHclust")': generates the
          actual graphic for this object. 

     _p_r_i_n_t 'signature(x = "clusterVisualHclust")': prints generic
          information  about the object. 

_A_u_t_h_o_r(_s):

     Gunnar Wrobel, <URL: http://www.gunnarwrobel.de>.

_S_e_e _A_l_s_o:

     'prepareAxis', 'goCluster-class', 'clusterModule-class',
     'clusterVisual-class'

_E_x_a_m_p_l_e_s:

     set.seed(1000)

     data(benomylsetupsmall)

     benomylsetupsmall$classalgo <- "clusterAlgorithmHclust"
     benomylsetupsmall$algo$method   <- "complete"
     benomylsetupsmall$algo$distance <- "euclidean"

     benomylsetupsmall$classvisu <- "clusterVisualHclust"

     a <- new("goCluster")

     execute(a) <- benomylsetupsmall

     if(interactive()){
     ## This example can only be run in an interactive mode

     ## This plot shows only one labeled region since the 
     ## loaded dataset has been reduced to only 100 genes. 
     ## Try the same with the full dataset
     display(a, selection = 1)
     }

