checkerboard           package:globaltest           R Documentation

_C_h_e_c_k_e_r_b_o_a_r_d _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 visualize the test result produced by
     'globaltest', by showing the association between pairs of samples.

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

     checkerboard(gt, geneset, sort = TRUE, 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)

    sort: A logical flag to indicate whether the samples should be
          sorted by the clinical outcome to give a clearer picture.

drawlabels: Logical value to control drawing of the samplenames on the
          x- and y-axis of the plot.

labelsize: Relative size of the labels on the x- and y-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 checkerboard shows the pairs of samples which have high
     covariance in white and the pairs with low covariance in black.
     This can be used to visualize the data and to search for outlying
     arrays.

     The left and bottom margins are adjusted to allow enough space for
     the longest samplename.

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

     A matrix giving the old and the new sample numbers.

_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', 'geneplot'.

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

         # Breast cancer data (exprSet) from the Netherlands Cancer
         # Institute with annotation:
         data(vandeVijver)
         data(annotation.vandeVijver)
         aPathway <- annotation.vandeVijver[1]

         gt <- globaltest(vandeVijver, "ESR1", aPathway)

         if (interactive()){
           checkerboard(gt[1])
         }

