imageplot             package:beadarray             R Documentation

_i_m_a_g_e_p_l_o_t _f_o_r _B_e_a_d_A_r_r_a_y_s _o_b_j_e_c_t

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

     Plots an image plot of a bead level data object.

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

     imageplot(BLData, array = 1, nrow = 18, ncol = 2, low= NULL,
     high = NULL, ncolors = 123, whatToPlot="G",zlim=NULL,...)

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

  BLData: Object of class BLData

   array: array to plot

    nrow: How many rows should the array be divided into

    ncol: How many columns should the array be divided into

     low: Color for area of lowest intensity

    high: color for area of highest intensity

 ncolors: The number of color graduations between high and low

whatToPlot: string identifying which matrix in BLData to use in the
          imageplot

    zlim: numerical vector of length 2 giving the extreme values of 'z'
          to associate with  colors 'low' and 'high'.

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

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

     Because of the high volume of bead level data, this function works
     by mapping a grid (who's size is specified by the nrow and ncol)
     arguments and averages the intensities of the beads within each
     section of this grid.

     The number of rows and columns may change the appearance of the
     plots. If the array is divided into too many sqaures it will
     difficult to detect changes.  We recommend using nrow=200 and
     ncol=20 for whole genome arrays

     An imageplot of the forgeround intensities is produced be default.
     Other matrices in BLData can be plotted by using the whatToPlot
     argument. eg change to Gb to plot the background intensities.

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

     Plot is produced on current graphical device.

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

     Mike Smith, Mark Dunning

