plotLocation              package:affy              R Documentation

_P_l_o_t _a _l_o_c_a_t_i_o_n _o_n _a _c_e_l _i_m_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Plots a location on a previously plotted cel image. This can be
     used to locate the physical location of probes on the array.

_U_s_a_g_e:

     plotLocation(x, col="green", pch=22, ...)

_A_r_g_u_m_e_n_t_s:

       x: a `location'. It can be obtained by the method of 'AffyBatch'
          'indexProbes', or made elsewhere (basically a location is
          nrows and two columns array. The first column corresponds to
          the x positions and the second columns corresponds to the y
          positions of n elements to locate)

     col: colors for the plot

     pch: plotting type (see function 'plot')

     ...: Other parameters passed to the function 'points'

_A_u_t_h_o_r(_s):

     Laurent

_S_e_e _A_l_s_o:

     'AffyBatch'

_E_x_a_m_p_l_e_s:

       ## loading data
       data(affybatch.example)

       ## image of the celfile
       image(affybatch.example[1])

       ## genenames, arbitrarily pick the 101th
       n <- geneNames(affybatch.example)[101]

       ## get the location for the gene n
       l <- indexProbes(affybatch.example, "both", n)[[1]]
       ## convert the index to X/Y coordinates
       xy <- indices2xy(l, abatch=affybatch.example) 

       ## plot
       plotLocation(xy)