pairs-methods              package:lumi              R Documentation

_P_a_i_r _p_l_o_t _o_f _a_n _E_x_p_r_e_s_s_i_o_n_S_e_t _o_b_j_e_c_t

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

     Creating 'pairs' plot of sample intensities in an ExpressionSet
     object

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

     ## S4 method for signature 'ExpressionSet':
     pairs(x, ..., smoothScatter = FALSE, logMode = TRUE, subset = 5000, main = NULL)

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

       x: a 'ExpressionSet' object

     ...: optional arguments to 'pairs'.

smoothScatter: whether use 'smoothScatter' function to plot points

 logMode: whether plot the data in log2 scale 

  subset: subset of rows used to plot. It can be an index vector, or
          the length of a random subset

    main: title of the plot 

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

     To increase the plot efficiency, by default, we only plot RANDOMLY
     selected subset of points (based on parameter "subset"). If users
     want to plot all the points, they can set the parameter "subset =
     NULL". When smoothScatter is set as TRUE, the subsetting will be
     suppressed because 'smoothScatter' function has good plot
     efficiency for large number of points.

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

     'LumiBatch-class', 'pairs'

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

     ## load example data
     data(example.lumi)

     pairs(example.lumi)

     if (require(geneplotter))
             pairs(example.lumi, smoothScatter=TRUE)

