plotArguments            package:siggenes            R Documentation

_P_l_o_t _A_r_g_u_m_e_n_t_s

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

     Utility function for generating a plot of a SAM or an EBAM object
     in an html output.

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

       plotArguments(pos.stats = NULL, sig.col = 3, xlim = NULL, ylim = NULL,
             main = NULL, xlab = NULL, ylab = NULL, pty = "s", lab = c(10, 10, 7),
             pch = NULL, sig.cex = 1, stats.cex = 0.8, y.intersp = 1.3)

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

pos.stats: an integer between 0 and 2 for a SAM plot, and between 0 and
          4 for an EBAM plot. See 'help.sam(plot)' or
          'help.ebam(plot)', respectively, for how 'pos.stats' can be
          specified, and for its default.

 sig.col: a specification of the color of the significant genes. If
          'sig.col' has length 1, all the points corresponding to
          significant genes are marked in the color specified by
          'sig.col'. Only for a SAM plot: If 'length(sig.col) == 2', 
          the down-regulated genes, i.e. the genes with negative
          expression score d, are marked in the color specified by
          'sig.col'[1], and the up-regulated genes, i.e. the genes with
          positive d, are marked in the color specified by
          'sig.col'[2].  For a description of how colors are specified,
          see 'par'.

    xlim: a numeric vector of length 2 specifying the x limits (minimum
          and maximum) of the plot.

    ylim: a numeric vector of length 2 specifying the y limits of the
          plot.

    main: a character string naming the main title of the plot.

    xlab: a character string naming the label of the x axis.

    ylab: a character string naming the label of the y axis.

     pty: a character specifying the type of plot region to be used.
          '"s"' (default for a SAM plot) generates a square plotting
          region, and '"m"' (default for an EBAM plot) the maximal
          plotting region.

     lab: a numeric vector of length 3 specifying the approximate
          number of tickmarks on the x axis and on the y axis and the
          label size.

     pch: either an integer specifying a symbol or a single character
          to be used as the default in plotting points. For a
          description of how 'pch' can be specified, see 'par'.

 sig.cex: a numerical value giving the amount by which the symbols of
          the significant genes should be scaled relative to the
          default.

stats.cex: the size of the statistics printed in the plot relative to
          the default size. Only available for an EBAM plot.

y.intersp: a numeric value specifying the space between the rows in
          which the statistics are plotted. Only available for an EBAM
          plot.

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

     A list required by 'sam2html' or 'ebam2html' if 'addPlot = TRUE'.

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

     Holger Schwender, holger.schw@gmx.de

_S_e_e _A_l_s_o:

     'sam2html','ebam2html'

