pvpick                package:pvclust                R Documentation

_F_i_n_d _C_l_u_s_t_e_r_s _w_i_t_h _H_i_g_h/_L_o_w _P-_v_a_l_u_e_s

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

     find clusters with relatively high/low p-values. 'pvrect' and
     'lines' (S3 method for class 'pvclust') highlight such clusters in
     existing plot, and 'pvpick' returns a list of such clusters.

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

     pvpick(x, alpha=0.95, pv="au", type="geq", max.only=TRUE)

     pvrect(x, alpha=0.95, pv="au", type="geq", max.only=TRUE, border=2, ...)

     ## S3 method for class 'pvclust':
     lines(x, alpha=0.95, pv="au", type="geq", col=2, lwd=2, ...)

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

       x: object of class 'pvclust'.

   alpha: threshold value for p-values.

      pv: character string which specifies the p-value to be used. It
          should be either of '"au"' or '"bp"', corresponding to AU
          p-value or BP value, respectively. See 'plot.pvclust' for
          details.

    type: one of '"geq"', '"leq"', '"gt"' or '"lt"'. If '"geq"' is
          specified, clusters with p-value _greater than or equals_ the
          threshold given by '"alpha"' are returned or displayed.
          Likewise '"leq"' stands for _lower than or equals_, '"gt"'
          for _greater than_ and '"lt"' for _lower than_ the threshold
          value. The default is '"geq"'.

max.only: logical. If some of clusters with high/low p-values have
          inclusion relation, only the largest cluster is returned (or
          displayed) when 'max.only=TRUE'.

  border: numeric value which specifies the color of borders of
          rectangles.

     col: numeric value which specifies the color of lines.

     lwd: numeric value which specifies the width of lines.

     ...: other graphic parameters to be used.

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

     'pvpick' returns a list which contains the following values. 

clusters: a list of character string vectors. Each vector corresponds
          to the names of objects in each cluster.

   edges: numeric vector of edge numbers. The i'th element (number)
          corresponds to the i'th name vector in 'clusters'.

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

     Ryota Suzuki ryota.suzuki@is.titech.ac.jp

