interactivePlots          package:beadarray          R Documentation

_I_n_t_e_r_a_c_t_i_v_e _b_e_a_d _l_e_v_e_l _p_l_o_t_t_i_n_g

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

     Plots using bead level data to discover spatial effects and
     artifacts on arrays

_U_s_a_g_e:

     SAMSummary(BLData, mode="outliers", missing_arrays=NULL, colour=TRUE, scale = NULL,...)
     BeadChipSummary(BLData,  mode="outliers",colour=TRUE, scale = NULL,...)

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

  BLData: BeadLevelList object

    mode: character string either "outliers", "fg", or "bg" specifying
          what to display on the plots

   scale: numeric value giving the amount by which to divide all
          numbers by (eg for log2 intensities this should be 16) to
          transform to range 0 - 1

missing_arrays: vector of numeric values specifying the index of any
          arrays that have been removed from the SAM.

  colour: if TRUE the hexagons will be plotted in colour

     ...: other graphical parameters to plot that can be specified

_D_e_t_a_i_l_s:

     A plot will be displayed giving a summary of each array in the
     experiment on the left screen and initially a blank right hand
     side. The left hand side is coloured according to the number of
     outliers found on the array or the mean intensity of the array
     (depending on the mode parameter). Clicking on tha particular 
     array on the left will display a location plot of the outliers or
     an image plot on the right

     See RNews article

_V_a_l_u_e:

     Plot will be produced on the current graphical device

_A_u_t_h_o_r(_s):

     Mark Dunning

