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 _o_n _a _S_A_M

_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.

     The values in v could be the values of a particular control probe
     across all arrays which can be obtained by the getMeanIntensities
     function.  The findAllOutliers function could also be used
     repeatedly for all arrays and then plotted using this function.

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

     Plot is produced on current graphical device.

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

     Mark Dunning

