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, plot = TRUE, addlegend = TRUE, ...)

_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

    plot: If 'FALSE': does not plot, but only returns a 'gt.barplot'
          object.

addlegend: If 'FALSE': does not add a legend to the plot or to the
          'gt.barplot' object.

     ...: 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:

     For references, type: citation("globaltest"). See also the
     vignette GlobalTest.pdf included with this package.

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

     'globaltest', 'sampleplot'.

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

         # Breast cancer data (exprSet) from the Netherlands Cancer
         # Institute with annotation:
         data(vandeVijver)
         data(annotation.vandeVijver)

         gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)

         if (interactive()){
           geneplot(gt["cell cycle checkpoint"])
         }

         gp <- geneplot(gt["cell cycle checkpoint"], plot = FALSE)
         if (interactive()){
           plot(sort(gp))
         }

