volcanoplot-methods           package:xps           R Documentation

_V_o_l_c_a_n_o _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Produce a scatter plot of fold-change values vs p-values, called
     volcano plot.

     _Usage_

     ' volcanoplot(x, labels      = "", p.value     = "pval", mask     
       = FALSE, show.cutoff = TRUE, cex.text    = 0.7, col.text    =
     "blue", col.cutoff  = "grey", xlim        = NULL, xlab        =
     "Log2(Fold-Change)", ylab        = "-Log10(P-Value)", pch        
     = '.', ...)  '

_A_r_g_u_m_e_n_t_s:

       x: object of class 'AnalysisTreeSet'.

  labels: optional transcript labels to be drawn at plotting points.

 p.value: type of p-value, 'pval' for p-value, 'padj' for adjusted
          p-value, or 'pcha' for p-chance.

    mask: logical, if 'TRUE' draw only points for transcripts
          satisfying the univariate test.

show.cutoff: logical, if 'TRUE' draw lines indicating cutoff.

cex.text: magnification to be used for optional 'labels'.

col.text: color to be used for optional 'labels'.

col.cutoff: color to be used for lines indicating cutoff, if
          'show.cutoff=TRUE'.

    xlim: optional range for the plotted fold-change values.

    xlab: label of x-axis.

    ylab: label of y-axis.

     pch: either an integer specifying a symbol or a single character
          to be used as the default in plotting points.

     ...: optional arguments to be passed to 'plot'.

_D_e_t_a_i_l_s:

     Produces a volcano plot for slot 'data' for an object of class
     'AnalysisTreeSet'.

     It is possible to label the points of the volcano plot, whereby
     the following 'labels' parameters are valid:

         'fUnitName':    unit name (probeset ID).
         'fName':        gene name.
         'fSymbol':      gene symbol.
         'fChromosome':  chromosome.
         'fCytoBand':    cytoband.

_A_u_t_h_o_r(_s):

     Christian Stratowa

