plot.confband.points           package:sma           R Documentation

_H_i_g_h_l_i_g_h_t_s _a _S_e_t _o_f _P_o_i_n_t_s _o_n _t_h_e _C_u_r_r_e_n_t _M _v_s _A _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function highlights a prespecified proportion of extreme
     points on the M vs A plots.

_U_s_a_g_e:

     plot.confband.points(x, M, crit1=0.025, crit2=crit1, nclass=10, col.ex, ...)

_A_r_g_u_m_e_n_t_s:

       x: a vector giving the x-coordinates of the points in the
          scatter plot. In the microarray context, this could be a
          vector of average log intensities. ie A

       M: a vector giving the y-coordinates of the points in the
          scatter plot. In the microarray context, this could be a
          vector of log intensity ratios.

   crit1: The number of points to be highlighted on the M vs A plot. If
          crit1 < 1, the crit1*100% spots with the smallest M values
          will be highlighted. If crit1 >= 1, the crit spots with the
          smallest M values are highlighted.

   crit2: Similar to "crit1".   If crit2 < 1, the crit2*100% spots with
          the largest M values will be highlighted. If crit2 >= 1, the
          crit2 spots with the smallest M values are highlighted.

  nclass: A single number giving the approximate number of intensity
          depedent groups to consider.

  col.ex: A color for extreme points

     ...: graphical parameters may also be supplied as arguments to the
          function (see 'par').

_V_a_l_u_e:

     Points are added to the current plot.

_N_o_t_e:

     An M vs A plot must be constructed *prior* to the execution of
     this function.

_S_e_e _A_l_s_o:

     'plot.mva', 'stat.ma', 'lines', 'matlines', 'plot.confband.text',
     'plot.confband.lines' .

_E_x_a_m_p_l_e_s:

     data(MouseArray)
     ## mouse.setup <- init.grid()
     ## mouse.data <- init.data()

     plot.mva(mouse.data, mouse.setup) ## an M vs A plot 

     mouse.lratio <- stat.ma(mouse.data, mouse.setup)

     plot.confband.points(mouse.lratio$A, mouse.lratio$M)

     ## 2.5% of the spots with the smallest and largest M values are
     ## highlighted on the M vs A plot. 

