plotFindArguments          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 the posterior
     probabilities in an html file when searching for the optimal value
     of the fudge factor in an  EBAM analysis.

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

       plotFindArguments(onlyTab = FALSE, logit = TRUE, pos.legend = NULL,
             legend.cex = 0.8, col = NULL, main = NULL, xlab = NULL, ylab = NULL,
             only.a0 = FALSE, lty = 1, lwd = 1, y.intersp = 1.1)

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

 onlyTab: if 'TRUE', then this plot is not generated and only the table
          of the number of differentially expressed genes and the
          estimated FDR for the different values of the fudge factor is
          shown

   logit: should the posterior probabilities be logit-transformed
          before they are plotted?

pos.legend: an integer between 0 and 4. See 'help.finda0(plot)' for how
          'pos.legend' can be specified, and for its default

legend.cex: the size of the text in the legend relative to the default
          size

     col: a vector specifying the colors of the lines for the different
          values of the fudge factor. For a description of how colors
          can be specified, see 'par'

    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

 only.a0: if 'TRUE', only the values of a0 are shown in the legend. If
          'FALSE', both the values of a0 and the corresponding number
          of differentially expressed genes are shown

     lty: a value or vector specifying the line type of the curves. For
          details, see 'par'

     lwd: a numeric value specifying the width of the plotted lines.
          For details, see 'par'

y.intersp: a numeric value specifying the space between the rows of the
          legend

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

     a list required by 'ebam2html' if 'findA0' is specified

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

     Holger Schwender, holger.schw@gmx.de

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

     'ebam2html'

