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:

     Generates spatial plots using bead-level data to discover
     artefacts on strips/arrays.

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

     SAMSummary(BLData, mode = "outliers", whatToPlot = "G",  samID = NULL, 
                    log = TRUE, n = 3, colour = TRUE,
                    scale = NULL, low = "yellow", high="red", ...)
     BeadChipSummary(BLData, mode = "outliers", whatToPlot = "G", chipID = NULL, 
                    stripsPerChip = 12, log = TRUE, n = 3, colour = TRUE, 
                    scale = NULL, low = "yellow", high = "red", ...)

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

  BLData: 'BeadLevelList' object

    mode: character string either "outliers" or "intensities"
          specifying what to display on the plots

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

   samID: character string specifying which SAM to plot.  If 'NULL',
          data from the first SAM is plotted.

  chipID: character string specifying which BeadChip to plot.  If
          'NULL', data from the first BeadChip is plotted.

stripsPerChip: integer specifying number of strips on BeadChip (8 or
          12)

     log: if TRUE log2 intensities of each bead are used to find
          outliers

       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

  colour: if TRUE the hexagons will be plotted in colour

   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

     low: colour to use for lowest intensity

    high: colour to use for highest intensity

     ...: other parameters to 'imageplot' 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:

     A plot is produced on the current graphical device

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

     Mark Dunning

