drawVolcanoPlot             package:maDB             R Documentation

_D_r_a_w _a _v_o_l_c_a_n_o _p_l_o_t

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

     'drawVolcanoPlot' plots a volcano plot scattering the M values
     (log2 ratio) on the x axis against the p value (-log10 the p
     value).

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

     drawVolcanoPlot(M,p,m=1,p.cut=0.05,p.transform=log10,ylab=NULL,colramp=NULL,na.rm=TRUE,...)

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

       M: The M values.

       p: The test statistics (usually p values).

       m: Where vertical lines should be drawn. By default two
          horizontal lines (at M=1 and M=-1) are added to the plot.
          Submit m=NA if none should be drawn.

   p.cut: For what p value a horizontal line should be added to the
          plot (by default for a p value of p=0.05). Specify p.cut=NA
          if no line should be drawn.

p.transform: The function that should be applied to the p values. By
          default '-log10'. Note a '-' is added to each function
          submitted here.

    ylab: The label for the y axis. By default '-log10(p)'

 colramp: A color ramp (set of colors) that should be used to code the
          local point desity. This attribute requires the package
          'geneplotter' as the 'densCols' function is used to calculate
          the local point density.

   na.rm: If NA values should be removed.

     ...: Additional parameters for the plot function.

_D_e_t_a_i_l_s:

     This function plots M values against test statistics. A horizontal
     line for a specific p value (by default 0.05) is added as well as
     vertical lines for a specific M value (by default 1 and -1). The
     data points can be colored according to the local point density by
     specifying a specific color ramp (e.g. 'colramp=topo.colors').

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

     Johannes Rainer

_R_e_f_e_r_e_n_c_e_s:

