viewBeads             package:beadarray             R Documentation

_V_i_e_w _B_e_a_d_s

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

     View an image of the beads in a certain region, optionally with
     links between neighbours or certain beads highlighted.

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

     viewBeads(BLData, array, x, y, xwidth = 100, ywidth = 100, neighbours = NULL, mark = NULL, markcol = "blue", markpch = 21, inten = TRUE, low = "black", high = "green", what = "G", log = TRUE, zlim = NULL, ...)

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

  BLData: 'BeadLevelList'

   array: integer specifying which strip/array to plot

       x: numeric value - x co-ordinate to centre on

       y: numeric value - y co-ordinate to centre on

  xwidth: numeric value - width of square

  ywidth: numeric value - width of square

neighbours: Neighbours matrix (optional) - if specified, links will be
          drawn between neighbours. (See 'generateNeighbours'.)

    mark: integral vector (optional) - a list of beadIDs to highlight.

 markcol: The colour used for the highlighted beads.

 markpch: The colour used for the highlighted beads.

   inten: logical - if true, plot coloured circles, with shades
          corresponding to intensities. Intensities are retrieved using
          'getArrayData', and the arguments below.

     low: Colour used for low intensities.

    high: Colour used for high intensities.

    what: Data to be used - passed to 'getArrayData'.

     log: Data to be used - passed to 'getArrayData'.

    zlim: Limits to be used. Supply in form c(0,5).

     ...: Additional arguments passed to 'getArrayData'.

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

     viewBeads plots the beads within the defined square region.

     Specifying a 'neighbours' matrix will result in links between
     neighbours being plotted. Specifying a 'mark' vector of beadIDs
     will result in the beads with these beadIDs being highlighted with
     a blue circular border.

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

     Outputs to the active graphical device.

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

     Jonathan Cairns

_S_e_e _A_l_s_o:

     'generateNeighbours'

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

     ##data(BLData)
     ##o <- findAllOutliers(BLData,2)

     ##x11()
     ##viewBeads(BLData, 2, 1000,1200,250,250, mark = o) ## outliers in this ##region are marked in blue
     ##x11()
     ##viewBeads(BLData, 2, 1000,1200,250,250, mark = o, inten = FALSE) ## ##removing the intensities makes the outlier locations easier to see

     ##neighbours <- generateNeighbours(BLData, 2)
     ##x11()
     ##viewBeads(BLData, 2, 1000,1200,250,250, neighbours) ## observe that ##there are many missing beads in this region, affecting the neighbours ##algorithm

