plot.confband.text            package:sma            R Documentation

_A_d_d _S_e_l_e_c_t_e_d _T_e_x_t _t_o _a_n _M _v_s _A _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     `text' draws the strings given in the vector `labs' at the
     coordinates given by `M' and `A'

_U_s_a_g_e:

     plot.confband.text(x, M, crit1=0.025, crit2=crit1, nclass=10,
     labs=NULL, output=FALSE, ...)  

_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 largest M values are highlighted.

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

    labs: one or more character strings or expressions specifying the
          text to be written.  If this string is not specified, by
          default the index of the vector `M' will be used.

  output: logical, defaulting to `FALSE'. If `TRUE' a vector
          containning the index to the vector `M' that are  
          highlighted.

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

_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.lines',
     'plot.confband.points' .

_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.text(mouse.lratio$A, mouse.lratio$M)
     ## 2.5% of the spots with the largest and smallest M values are
     ## highlighted on the M vs A plot, and each spot is assigned the
     ## default label of its corresponding index value. 

