plotMA3by2               package:limma               R Documentation

_W_r_i_t_e _M_A-_P_l_o_t_s _t_o _F_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Write MA-plots to files in PNG format, six plots to a file in a 3
     by 2 grid arrangement.

_U_s_a_g_e:

     plotMA3by2(MA, prefix="MA", path=NULL, main=colnames(MA), zero.weights=FALSE, common.lim=TRUE, device="png", ...)

_A_r_g_u_m_e_n_t_s:

      MA: an 'MAList' or 'RGList' object, or any list with components
          'M' containing log-ratios and 'A' containing average
          intensities

  prefix: character string giving prefix to attach to file names

    path: character string specifying directory for output files

    main: character vector giving titles for plots

zero.weights: logical, should points with non-positive weights be
          plotted

common.lim: logical, should all plots on a page use the same axis
          limits

  device: device driver for the plot. Choices are '"png"', '"jpeg"',
          '"pdf"', '"postscript"'.

     ...: any other arguments are passed to 'plotMA'

_D_e_t_a_i_l_s:

     This function writes a series of graphic files to disk. Each file
     contains six MA-plots in three rows and two columns. The layout is
     optimized for A4-sized paper.

     The graph format can be '"png"' or '"jpeg"', which are
     screen-resolution formats, or '"pdf"' or '"postscript"', which are
     loss-less formats. '"png"' is not available on every R platform.
     Note that '"pdf"' or '"postscript"' may produce very large files.

_V_a_l_u_e:

     No value is returned, but one or more files are written to the
     working directory. The number of files is determined by the number
     of columns of 'MA'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of diagnostic functions available in LIMMA is given in
     09.Diagnostics.