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 = 100, ncol = 100, low= NULL,
                high = NULL, ncolors = 123, whatToPlot ="G", log=TRUE,
                zlim=NULL, main=whatToPlot, method="illumina", n = 3,
                trim=0.05, legend=TRUE, ...)

_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/values to
          plot. See 'getArrayData' for a list of the possibilities

     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

  method: chracter string specifying the summarisation method to use.
          Only applicable when 'whatToPlot="residG"', '"residR"' or
          '"residM"'. Refer to help 'createBeadSummaryData' help page
          for further information.

       n: use n median absolute deviations from the median as a cut-off
          for outliers.  Only applicable when 'whatToPlot="residG"',
          '"residR"' or '"residM"'. Refer to help
          'createBeadSummaryData' help page for further information.

    trim: fraction of intensities to remove from the bead summary
          calculations.  Only applicable when 'whatToPlot="residG"',
          '"residR"' or '"residM"'.  Refer to 'createBeadSummaryData'
          help page for further information.

  legend: logical, if 'TRUE', 'zlim' and range of data is added to
          plot.

     ...: 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 squares it will be
     difficult to detect changes. We recommend using 'nrow=20' and
     'ncol=200' for whole genome arrays, and 'nrow=100' 'ncol=100' for
     arrays on a SAM.

     An imageplot of the log base 2 foreround intensities is produced
     by default. Other values can be plotted by changing the
     'whatToPlot' 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)

