plotDensity               package:affy               R Documentation

_P_l_o_t _D_e_n_s_i_t_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Plots the non-parametric density estimates using values contained
     in the columns of a matrix.

_U_s_a_g_e:

     plotDensity(mat, ylab = "density", xlab="x", type="l", col=1:6,
                 na.rm = TRUE, ...)

     plotDensity.AffyBatch(x, col = 1:6, log = TRUE,
                           which=c("pm","mm","both"),
                           ylab = "density",
                           xlab = NULL, ...)

_A_r_g_u_m_e_n_t_s:

     mat: A matrix containing the values to make densities in the
          columns.

       x: A object of clase 'AffyBatch'

     log: logical value. If 'TRUE' the log of the intensities in the
          'AffyBatch' are plotted.

   which: should a histogram of the PMs, MMs, or both be made?

     col: The colors to use fot the different arrays

    ylab: a title for the y axis.

    xlab: a title for the x axis.

    type: type for the plot.

   na.rm: handling of 'NA' values.

     ...: graphical parameters can be given as arguments to 'plot'

_D_e_t_a_i_l_s:

     The list returned can be convenient for plotting large input
     matrices with different colors/line types schemes (the computation
     of the densities can take some time).

     To match other functions in base R, this function should probably
     be called 'matdensity', as it is sharing similarities with
     'matplot' and 'matlines'.

_V_a_l_u_e:

     It returns invisibly a list of two matrices `x' and `y'.

_A_u_t_h_o_r(_s):

     Ben Bolstad and Laurent Gautier

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)
       plotDensity(exprs(Dilution), log="x")
     }

