plotBeadLocations         package:beadarray         R Documentation

_S_h_o_w _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 an array. The beads can either
     be defined to be all beads with particular ProbeIDs or individual
     beadIDs

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

     plotBeadLocations(BLData, ProbeIDs=NULL, BeadIDs=NULL, array, SAM=FALSE,...)

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

  BLData: a BeadLevelList object

ProbeIDs: a vector of ProbeIDs to plot

 BeadIDs: a vector of beadIDs to plot

   array: numeric value specifying the array

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

     ...: 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:

     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, ProbeIDs=2, array=1)

     #plot all beads with either ProbeID 2 or 10

     plotBeadLocations(BLData, ProbeIDs=c(2, 10), array=1)

     #can also change plotting characters

     plotBeadLocations(BLData, ProbeIDs=c(2, 10), array=1, col="red", pch="X", cex=2)

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

     plotBeadLocations(BLData, beadIDs=o, array=1)

