plotMA               package:codelink               R Documentation

_M_A _p_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Takes a Codelink object and plot M vs A.

_U_s_a_g_e:

       plotMA(object, array1 = 1, array2 = NULL, cutoff = c(-1, 1), label = NULL,
         type = NULL, high.list = NULL, high.col = "blue", high.pch = 21,
             high.bg = "cyan",       snr = NULL, snr.cutoff = 1, legend.x = NULL, pch = ".", 
             subset = NULL, title = NULL, xlim = NULL, ylim = NULL)

_A_r_g_u_m_e_n_t_s:

  object: an object of class "Codelink" or "MAarrayLM".

  array1: first array to be used.

  array2: second array to be used.

  cutoff: cutoff to be used as fold change markeer.

   label: type of labeling used in legend.

    type: spot type information.

high.list: list of genes highlighted.

high.col: color used for high genes.

high.pch: pch used for high genes.

 high.bg: background color used for high genes.

     snr: vector with SNR values, usually, taking rowMeans() from a SNR
          matrix.

snr.cutoff: SNR cutoff used for label spots.

legend.x: relative position of the legend.

     pch: pch style used to main spots.

  subset: subset of spots used to plot based on 'type' slot.

   title: title of the plot.

    xlim: range for the X axis.

    ylim: range for the Y axis.

_D_e_t_a_i_l_s:

     This function has suffered recent re-working, to increase the
     usability and  to clean a little bit the code.

     If array2 is NULL a median array is computed using all available
     arrays.   Then the values of M and A are computed using the
     following formula:

     M = array2 - array1

     A = (array2 + array1) / 2

     If type information is available in the Codelink object, or
     provided throught the 'type' argument, spots are colored based on
     that. DISCOVERY spots are  plotted black with pch = "." whereas
     the other classes are plotted with  different background colors,
     using gray as border to increase contrasts. For  that pch = 21 is
     used. If snr is specified as label option, the SNR is used  to
     label spots, if available in the Codelink object. In this case,
     the mean  SNR across all arrays is used when array2 = NULL.

     Some parameters may not be working right now, as the new function
     is using a  different method to labels spots.

     The legend is 'automagically' located, but this can be overrided
     with the  legend.x argument.

     In addition, a subset of the spots can be plotted based on type
     information  when available. This allows, for example, to plot
     only DISCOVERY spots.

_A_u_t_h_o_r(_s):

     Diego Diez

_E_x_a_m_p_l_e_s:

     ## Not run: 
         data(codelink.example)
         plotMA(codelink.example)
     ## End(Not run)

