plotRG               package:beadarray               R Documentation

_P_l_o_t _b_e_a_d _l_e_v_e_l _d_a_t_a: _R _v_s _G _i_n_t_e_n_s_i_t_i_e_s

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

     Shows R and G intensities fom a BeadLevelList object. The beads
     can either be defined to be all beads with particular ProbeIDs or
     rows BeadIDs

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

     plotRG(BLData, ProbeIDs=NULL, BeadIDs=NULL, log=TRUE, arrays=1,
                        xlim=c(8,16), ylim=c(8,16), xlab="G intensities",
                        ylab="R intensities",
                        main=arrayNames(BLData)[arrays], smooth=TRUE,
                        cols=NULL, ...)

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

  BLData: a BeadLevelList object

ProbeIDs: a vector of ProbeIDs to plot

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

     log: logical, if TRUE, take log base 2 of intensities

  arrays: which array/s to plot

    xlim: x-axis limits for plot

    ylim: y-axis limits for plot

    xlab: character string specifying x-axis label

    ylab: character string specifying y-axis label

    main: main plot title

  smooth: logical, whether to smooth the points (only used when one
          array is selected for plotting)

    cols: colours to use on the plot

     ...: further graphical parameters to 'plot'

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

     The R and G intensities from selected beads and arrays are
     plotted.

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

     Plot is produced on the current graphical device.

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

     Matt Ritchie

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

     data(BLData)

     #plot all beads from array 1
     plotRG(BLData, arrays=1)

     #plot Beads with ProbeIDs 2 on arrays 1-4
     plotRG(BLData, arrays=1:4, ProbeIDs=1000, pch=16)

