density-methods             package:lumi             R Documentation

_D_e_n_s_i_t_y _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 density plot of sample intensities in a ExpressionSet
     object. It is equivalent to hist-methods.

_U_s_a_g_e:

     ## S4 method for signature 'ExpressionSet':
     density(x, logMode=TRUE, xlab = NULL, ylab = "density", type = "l", 
             col=1:dim(x)[2], lty=1:dim(x)[2], lwd=1, xlim = NULL, index.highlight = NULL, color.highlight = 2, 
             symmetry = NULL, addLegend = TRUE, subset = 5000, seed = 123, ...)

_A_r_g_u_m_e_n_t_s:

       x: a 'ExpressionSet' object

 logMode: determine whether the density plot is based on a log2 scale 

    xlab: xlab of the density plot 

    ylab: ylab of the density plot 

    type: parameter of plot function 

     col: line colors of the density plot 

     lty: line types of the density plot 

     lwd: line width of plot function 

    xlim: parameter of the plot function

index.highlight: the column index of the highlighted density curve 

color.highlight: color of highlighted density curve 

symmetry: the boundary position suppose to be symmetric distributed  

addLegend: whether add legend to the plot or not 

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

    seed: the random seed for random subset

     ...: additional parameters for 'density' function 

_S_e_e _A_l_s_o:

     'LumiBatch-class', hist-methods, 'density'

_E_x_a_m_p_l_e_s:

     ## load example data
     data(example.lumi)

     density(example.lumi)

