arrayview              package:maanova              R Documentation

_V_i_e_w _t_h_e _l_a_y_o_u_t _o_f _i_n_p_u_t _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This function reconstructs the input data according to the
     Microarray grid location structure and plots the data according to
     the user specified color map.

     By default, it will plot the log ratios for 2-dye array and raw
     intensity for 1-dye array. It does not work for N-dye (N>2) array
     at this time.

     Note that if user collapsed the replicates by using 'avgrep' in
     'read.madata', and then  arrayview will not be available.

_U_s_a_g_e:

     arrayview(object, ratio, array, colormap, onScreen=TRUE, ...)

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'madata'.

   ratio: The data to be plotted. The length of it must be equal to the
          length of the grid locations, .e.g, madata$row and
          madata$col. If ratio is a vector, there will be one plot. If
          ratio is a matrix, there will be one plot for each column. If
          ratio is not provided, 'link[maanova]{make.ratio}' will be
          called to calculate the ratios from the original data.

   array: A list of arrays to be plotted. This variable is only valid
          when 'ratio' is not provided. Whenever 'ratio' is provided,
          all columns in ratio will be plotted.

colormap: User specified color map. See 'colors' for more detail.

     ...: Other parameters to be passed to 'image'.

onScreen: A logical value to represent whether to display the plots on
          screen or not. If TRUE, x11() (in Unix/Windows) or macintosh
          (in Mac) will be called inside the function. Otherwise, it
          will plot the figure on the current device. Default is TRUE.

_A_u_t_h_o_r(_s):

     Hao Wu

_E_x_a_m_p_l_e_s:

     ## Not run: 
     data(kidney)
     # arrayview data on screen
     arrayview(kidney.raw, array=1)
     graphics.off()
     # arrayview raw data array 1 and 3 and output to postscript file
     postscript(file="kidneyArrayview.ps")
     arrayview(kidney.raw, array=c(1,3), onScreen=FALSE)
     ## End(Not run)

