clusterVisualHeatmap-class     package:goCluster     R Documentation

_C_l_a_s_s "_c_l_u_s_t_e_r_V_i_s_u_a_l_H_e_a_t_m_a_p", _p_r_e_p_a_r_e_s _a _g_o_C_l_u_s_t_e_r _a_n_a_l_y_s_i_s _f_o_r
_v_i_s_u_a_l_i_z_a_t_i_o_n.

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

     The class will prepare the 'goCluster'-result for visualization.

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

     The class provides a wrapper around the 'prepareHeatmap'-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"', matches the "tree" structure
          of the annotation term selection from the significance
          analysis. But instead of a single annotation term each node
          holds a combination of the annotation term, the genes that
          were responsible for the selection of this annotation term
          and the expression values of these genes. 

     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 = "clusterVisualHeatmap")': interactive
          setup of the class. There are no options that you can set on
          this class.

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

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

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

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

     _p_r_i_n_t 'signature(x = "clusterVisualHeatmap")': 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:

     'prepareHeatmap', 'goCluster-class', 'clusterModule-class',
     'clusterVisual-class'

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

     set.seed(1000)

     data(benomylsetupsmall)

     benomylsetupsmall$classvisu <- "clusterVisualHeatmap"

     a <- new("goCluster")

     execute(a) <- benomylsetupsmall

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

     ## This plot shows only four genes since the loaded dataset
     ## has been reduced to only 100 genes. Try the same with
     ## the full dataset
     display(a, selection = "GO:0003735")
     }

