plot.stamFit              package:stam              R Documentation

_P_l_o_t_s _f_o_r _S_t_A_M _M_o_d_e_l _F_i_t

_D_e_s_c_r_i_p_t_i_o_n:

     Overall alpha vs. delta plot as well as nodewise scatter plots on 
     performance/redundancy and specificity/sensitivity.

_U_s_a_g_e:

     ## S3 method for class 'stamFit':
     plot(x, outfile = NULL, aclass = NULL, main = NULL,
                  which = 0, res = 72, ps = FALSE, pointsize = 12, ...)

_A_r_g_u_m_e_n_t_s:

       x: the object of type stamFit for which the plots are to be
          drawn

 outfile: name of output file if postscript or PNG graphics is to be
          generated.  The extension of the file is chosen automatically
          according to the 'ps'  argument. The filename is also
          augmented by suffixses to distinguish the plots  generated.
          If no outfile is specified, an interactive plot is attempted

  aclass: the name of the phenotype class of interest, usually the
          disease class

   which: choose the plot to be generated. 1:alpha vs. delta,
          2:nodewise evaluation,  0:both plots in interactive mode, non
          otherwise.

    main: the main title of the plot, generated automatically if left
          blank

     res: resolution in points per inch

      ps: if set to TRUE postscript output is generated

pointsize: the standard fontsize

     ...: additional arguments to be passed to plot

_D_e_t_a_i_l_s:

     If several values for alpha are provided to stam.fit plot.stamFit
     generates a compound  score vs. shrinkage level plot. For each
     alpha one line is drawn and the best shrinkage (where the minimum
     is achieved) is marked. In a second pane of the same plot alpha is
      plotted vs. these best shrinkage levels.

     Additionally nodewise scatter plots comparing performance vs. 
     redundancy and sensitivity vs. specificity are generated.

_A_u_t_h_o_r(_s):

     Claudio Lottaz

_S_e_e _A_l_s_o:

     'stam.fit'

