geneplot             package:globaltest             R Documentation

_G_e_n_e _P_l_o_t _f_o_r _G_l_o_b_a_l _T_e_s_t

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

     Produces a plot to show the influence of individual genes on the
     test result produced by 'globaltest'.

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

     geneplot(gt, geneset, genesubset, scale = FALSE, 
                 drawlabels = TRUE, labelsize = 0.6, ...)

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

      gt: The output of a call to 'globaltest'.

 geneset: The name or number of the geneset to be plotted  (only
          necessary if multiple genesets were tested).

genesubset: A vector of names or numbers of genes to be plotted 
          (default: plot all genes)

   scale: Logical: should the bars be scaled to unit standard
          deviation?

drawlabels: Logical value to control drawing of gene ids (rownames) on
          the x-axis of the plot.

labelsize: Relative size of the labels on the x-axis. If it is 'NULL' ,
           the current value for 'par("cex.axis")'  is used

     ...: Any extra arguments will be forwarded to the plotting 
          function.

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

     The geneplot shows a bar an a reference line for each  gene. The
     bar shows the influence of each gene on the test  result: the test
     statistic Q is the average of the bars of the  genes. The
     reference line shows the expected influence if the  gene was not
     associated with the outcome. The marks on the bars  show the
     standard deviation of the bar under the null hypothesis.  The
     color of the bar indicates positive or negative correlation  of
     the gene with the clinical outcome, to distinguish between up  and
     downregulation.

     The bottom margin is adjusted to allow enough space for the
     longest  gene id to draw under the axis.

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

     An object of type 'gt.barplot'.

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

     Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

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

     J. J. Goeman, S. A. van de Geer, F. de Kort and J. C.  van
     Houwelingen, 2004, _A global test for groups of genes:  testing
     association with a clinical outcome_,  _Bioinformatics_ 20 (1)
     93-99. See also the How To  Globaltest.pdf included with this
     package.

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

     'globaltest', 'sampleplot'.

_E_x_a_m_p_l_e_s:

         data(exampleX)      # Expression data (40 samples; 1000 genes)
         data(exampleY)      # Clinical outcome for the 40 samples
         pathway <- 1:25     # A pathway contains genes 1 to 25
         gt <- globaltest(exampleX, exampleY, test.genes = pathway)
         gt
         
         if (interactive()){ 
           geneplot(gt)
         }

