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", log=TRUE,
                zlim=NULL, main=whatToPlot, ...)

_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: character string specifying which intensities to plot.
          Possibilities are '"G"', '"Gb"' for single channel data and
          '"G"', '"Gb"', '"R"' and '"Rb"' for two-colour data

     log: if TRUE, log2 intensities are plotted

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

    main: character string for plot title

     ...: 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 (log base 2) 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 squares 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 intensities can be plotted by using the 'which' argument.

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

     Plot is produced on current graphical device.

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

     Mike Smith, Mark Dunning

_E_x_a_m_p_l_e_s:

     data(BLData)

     imageplot(BLData, nrow=100, ncol=100)

