plot.spatial               package:sma               R Documentation

_S_p_a_t_i_a_l _R_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _M_i_c_r_o_a_r_r_a_y _S_p_o_t _S_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Creates an image of shades of gray or colors, that represents the
     values of a statistic for each spot on the array. The statistic
     can be a log intensity ratio, quality information such as spot
     size or shape, or a t-statistic. This function can be used to
     explore whether there are any spatial effects in the data.

_U_s_a_g_e:

     plot.spatial(x, layout, crit1=0.05, crit2=crit1, ...)

_A_r_g_u_m_e_n_t_s:

       x: a numerical vector. This vector can contain any spot 
          statistics, such as log intensity ratios, spot sizes or
          shapes, or t-statistics.

  layout: a list specifying the dimensions of the spot matrix and the
          grid matrix. This can be generated by calling  'init.grid'.

   crit1: the number of values from x to be displayed on the image.  If
          crit1 < 1, the crit1*100% spots with the largest x values are
          displayed. If crit1 >= 1, the crit1 spots with the largest x
          values are displayed.

   crit2: the number of values from x to be displayed on the image. If
          crit2 < 1, the crit2*100% spots with the largest x values are
          displayed. If crit2 >= 1, the crit2 spots with the largest x
          values are displayed.

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

_D_e_t_a_i_l_s:

     The values that didn't meet the criteria are not shown on the
     image. The image follows the layout of an actual microarray slide
     with the top left corner representing the spot (1,1,1,1).

_V_a_l_u_e:

     An image is created on the current graphics device.

_N_o_t_e:

     'draw.image.func' and 'spatial.func' are called by 'plot.spatial'
     and are not typically  used on their own.

_A_u_t_h_o_r(_s):

     Yee Hwa Yang, yeehwa@stat.berkeley.edu 
      Sandrine Dudoit, sandrine@stat.berkeley.edu

_S_e_e _A_l_s_o:

     'draw.image.func', 'init.grid',  'spatial.func', 'image'.

_E_x_a_m_p_l_e_s:

     data(MouseArray)
     # mouse.setup <- init.grid()
     # mouse.data <- init.data() ## see \emph{init.data}

     mouse.lratio <- stat.ma(mouse.data, mouse.setup)
     plot.spatial(mouse.lratio$M[,1], mouse.setup) ## default 85

     # Looking for areas where the spots are not quite circular
     plot.spatial(mouse1[,"shape"], mouse.setup, crit1=0.1)

