plotOnSAM             package:beadarray             R Documentation

_S_h_o_w _v_a_r_i_a_t_i_o_n _b_e_t_w_e_e_n _a_l_l _9_6 _a_r_r_a_y_s

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

     Function to show how quantities vary across all 96 arrays. eg Mean
     intensity of a certain control probe

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

     plotOnSAM(values, mx = max(values, na.rm = TRUE), scale = max(values,
     na.rm = TRUE), min = 0, main = NULL, label = TRUE, missing_arrays = NULL, colour=TRUE)

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

  values: vector containing 96 numeric values to plot

      mx: maximum value to display on y axis of plot

   scale: numeric value giving the amount by which to divide all
          numbers by (eg for log2 intensities this should be 16) to
          transform to range 0 - 1

     min: numeric value giving the minimum value to display on y axis

    main: character string giving a title for the plot

   label: boolean defining if the arrays are labeled on the plot

missing_arrays: vector of numeric values specifying the index of any
          arrays that have been removed from the SAM.

  colour: if TRUE the hexagons will be plotted in colour

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

     Two plots are produced side-by-side. The first is a plot of the
     set of values against the index 1-96 and secondly we plot 8 x 12
     hexagonal arrays with array  number 1 being the hexagon in the
     top-left corner and array 96 in the bottom-right. The colour of
     hexagon is directly related to the value in v for the particular 
     array number. An array which has a higher value in v will be
     coloured brighter.

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

     Plot is produced on current graphical device.

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

     Mark Dunning

