rankedGenesImg-methods        package:Rmagpie        R Documentation

_r_a_n_k_e_d_G_e_n_e_s_I_m_g _M_e_t_h_o_d _t_o _p_l_o_t _t_h_e _g_e_n_e_s _a_c_c_o_r_d_i_n_g _t_o _t_h_e_i_r _f_r_e_q_u_e_n_c_y _i_n _a _m_i_c_r_o_a_r_r_a_y _l_i_k_e _i_m_a_g_e

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

     Generate an image per value of option representing the features
     (on dot per feature). The color of the dot depends on the
     frequency of the feature in for the given value of option (number
     of genes or threshold).

_A_r_g_u_m_e_n_t_s:

  object: 'Object of class assessment'. Object assessment of interest.

storagePath: 'character'. URL where the image must be stored.

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


     _o_b_j_e_c_t = "_a_s_s_e_s_s_m_e_n_t" The method is only applicable on objects of
          class assessment.

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

     ## Not run: 
     data('vV70genesDataset')

     expeOfInterest <- new("assessment", dataset=vV70genes,
                                        noFolds1stLayer=3,
                                        noFolds2ndLayer=2,
                                        classifierName="svm",
                                        typeFoldCreation="original",
                                        svmKernel="linear",
                                        noOfRepeat=10,
                                        featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,3,4,5,6)))

     expeOfInterest <- runOneLayerExtCV(expeOfInterest)

     rankedGenesImg(expeOfInterest, storagePath='myPath')
     ## End(Not run)

