MAplot-methods             package:lumi             R Documentation

_M_A_p_l_o_t _o_f _a _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 pairwise MAplot of sample intensities in a ExpressionSet
     object

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

  object: an 'ExpressionSet' object

     ...: optional arguments to 'MAplot'.

smoothScatter: whether use 'smoothScatter' function to plot points

 logMode: whether plot the data in log2 scale or not

  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', 'MAplot'

_E_x_a_m_p_l_e_s:

     ## load example data
     data(example.lumi)

     MAplot(example.lumi)

     MAplot(example.lumi, smoothScatter=TRUE)

