imageplot             package:beadarray             R Documentation

_i_m_a_g_e_p_l_o_t _f_o_r _B_e_a_d_L_e_v_e_l_L_i_s_t _o_b_j_e_c_t

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

     Generates an image plot for data from a 'BeadLevelList' 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, SAM=FALSE, ...)

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

  BLData: 'BeadLevelList'

   array: integer specifying which strip/array to plot

    nrow: integer specifying the number of rows to divide the
          strip/array into

    ncol: integer specifying the number of columns to divide the
          strip/array into

     low: colour to use for lowest intensity

    high: colour to use for highest intensity

 ncolors: The number of colour graduations between high and low

whatToPlot: character string specifying which intensities/values to
          plot. See 'getArrayData' for a list of possibilities

     log: if TRUE, log2 intensities are plotted

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

    main: character string for plot title

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

       n: numeric value specifying the number of median absolute
          deviations (MADs) from the median to use as a cut-off for
          outliers.  The default value is 3.  Only applicable when
          'whatToPlot="residG"', '"residR"' or '"residM"'  and
          'method="illumina"'.  Refer to '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.

     SAM: logical, if 'TRUE', x and y coordinates are transposed.

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

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

     Because of the large number of beads on each strip/array, this
     function works by mapping a grid of size specified by the 'nrow'
     and 'ncol' arguments and averaging the intensities of the beads
     within each section of the 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 the strips on a BeadChip, and 'nrow=100' 'ncol=100'
     for arrays on a SAM.

     An imageplot of the log base 2 foreground intensities is produced
     by default. Other values can be plotted by changing the
     'whatToPlot' argument. The default colour scheme ranges from white
     for low values to blue for high values.

     As a result of both having identical function names this function
     can conflict with the  'imageplot' method in 'limma'.  If both
     packages are loaded, the function from whichever package was
     loaded last takes precedence.  If the 'beadarray' imageplot()
     function is masking that from 'limma', one can directly call the
     'limma' method using the command "limma::imageplot()". 
     Alternatively, one can detach the 'beadarray' package using
     "detach(package:beadarray)".  Similar techniques can be used if
     'limma' is masking the 'beadarray' method.

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

     A plot is produced on the 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)

