plotBeadLocations         package:beadarray         R Documentation

_P_l_o_t _b_e_a_d _l_o_c_a_t_i_o_n_s

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

     Shows location of a set of beads on a strip/array. The beads can
     either be defined to be all beads with particular ProbeIDs or as
     rows in 'BeadLevelList'.

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

     plotBeadLocations(BLData, ProbeIDs = NULL, BeadIDs = NULL, array = 1,
                        SAM = FALSE, xlab = "x-coordinate",
                        ylab = "y-coordinate",
                        main = paste("Bead", ProbeIDs,"locations"), ...)

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

  BLData: 'BeadLevelList'

ProbeIDs: a vector of ProbeIDs to plot

 BeadIDs: logical/integer vector specifying which rows of data from
          'BeadLevelList') to plot (used if 'ProbeIDs' is 'NULL')

   array: integer specifying the strip/array to plot

     SAM: if TRUE then the data is assumed to be taken from a SAM array
          and therefore hexagonal

    xlab: character string specifying x-axis label

    ylab: character string specifying y-axis label

    main: character string specifying plot title

     ...: further graphical parameters to 'plot'

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

     The outline of the hexagonal array is drawn and the locations of
     the specified beads are overlayed.

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

     A plot is produced on the current graphical device.

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

     Mark Dunning

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

     data(BLData)

     #plot all beads with ProbeID 2 on array 1
     plotBeadLocations(BLData, array=1, ProbeIDs=2, SAM=TRUE)

     #find all outliers on the first array and plot their locations
     o=findAllOutliers(BLData, 1)
     plotBeadLocations(BLData, BeadIDs=o, array=1, SAM=TRUE)

