plotSmoothed           package:quantsmooth           R Documentation

_p_l_o_t_S_m_o_o_t_h_e_d

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

     Plot a smoothed line together with the original data values

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

       plotSmoothed(intensities, position, ylim=NULL, ylab="intensity", xlab="position", normalized.to=NULL, grid=NULL, smooth.lambda=2, interval=0.5, plotnew=TRUE, cols, cex.pts = 0.6, ...)

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

intensities: numeric vector or matrix, data are plotted by column

position: numeric vector; the length should be the number of rows in
          intensities

    ylim: numeric vector of length 2, limits for plot. If 'NULL' then
          the minimal and maximal value in 'intensities' is used

    ylab: character, label for y-position

    xlab: character, label for x-position

normalized.to: numeric, a line(s) is drawn at this horizontal position

    grid: numeric, a line(s) is drawn at this vertical position

smooth.lambda: numeric, smoothing parameter see 'quantsmooth'

interval: numeric (0..1), plotting of extra smoothed lines around
          median. With 'interval' = 0.5 the 0.25 and 0.75 quartiles are
          plotted, with 'interval' = 0.9 the 0.05 and 0.95 quantiles
          are plotted, 

 plotnew: logical, if TRUE a new plot is created, else the data are
          plotted into an existing plot

    cols: color vector, colors for columns in 'intensities' 

 cex.pts: size of the dots in the plot. Set to '0' to skip plotting the
          dots

     ...: extra parameters for 'plot'

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

     This function plots the raw data values as dots and the median
     smoothed values as a continuous line. If interval is supplied
     these are plotted as lines in different line types. More than 1
     interval can be given.

_V_a_l_u_e:

     This function is used for its side effects

_A_u_t_h_o_r(_s):

     Jan Oosting

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

     'quantsmooth'

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

              data(chr14)
              plotSmoothed(bac.cn,bac.pos,ylim=c(1,2.5),normalized.to=2,smooth.lambda=2.5)

