pmplot-methods              package:xps              R Documentation

_B_a_r_p_l_o_t _o_f _P_M _a_n_d _M_M _I_n_t_e_n_s_i_t_i_e_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Creates a barplot of mean perfect match and mismatch intensities.

     _Usage_

     ' pmplot(x, which = "", size = 0, transfo = NULL, method  =
     "mean", names = "namepart", beside = TRUE, col = c("red", "blue"),
     legend = c("PM","MM"), ...) '

_A_r_g_u_m_e_n_t_s:

       x: object of class 'DataTreeSet'.

   which: type of probes to be used, for details see 'validData'.

    size: length of sequence to be generated as subset.

 transfo: a valid function to transform the data, usually "log2", or
          "0".

  method: method to compute average intensities, "mean" or "median".

   names: optional vector of sample names.

  beside: logical. If 'FALSE', mean intensities are portrayed as
          stacked bars,  and if 'TRUE' the columns are portrayed as
          juxtaposed bars.

     col: color of PM, MM bars.

  legend: a vector of text used to construct a legend for the plot,  or
          a logical indicating whether a legend should be included.

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

_D_e_t_a_i_l_s:

     Produces barplots of mean perfect match and mismatch intensities
     for slot 'data' for an object of class 'ExprTreeSet'.

     For 'names=NULL' full column names of slot 'data' will be
     displayed while for  'names="namepart"' column names will be
     displayed without name extension. If 'names' is a vector of column
     names, only these columns will displayed as pmplot.

_N_o_t_e:

     Data must first be attached to class 'DataTreeSet' using method
     'attachInten'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'boxplot.dev', 'boxplot', 'barplot'

_E_x_a_m_p_l_e_s:

     ## load existing ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     ## need to attach scheme mask and probe intensities
     data.test3 <- attachMask(data.test3)
     data.test3 <- attachInten(data.test3)

     if (interactive()) {
     pmplot(data.test3)
     }

     ## optionally remove mask and data to free memory
     data.test3 <- removeInten(data.test3)
     data.test3 <- removeMask(data.test3)

