plot-methods              package:xcms              R Documentation

_P_l_o_t _e_x_t_r_a_c_t_e_d _i_o_n _c_h_r_o_m_a_t_o_g_r_a_m_s _f_r_o_m _m_u_l_t_i_p_l_e _f_i_l_e_s

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

     Batch plot a list of extracted ion chromatograms to the current
     graphics device.

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

       x: the 'xcmsEIC' object

       y: optional 'xcmsSet' object with peak integration data

groupidx: either character vector with names or integer vector with
          indicies of peak groups for which to plot EICs 

sampleidx: either character vector with names or integer vector with
          indicies of samples for which to plot EICs 

 rtrange: a two column matrix with minimum and maximum retention times
          between which to return EIC data points

          if it has the same number of rows as the number groups in the
          'xcmsEIC' object, then 'sampleidx' is used to subset it.
          otherwise, it is repeated over the length of 'sampleidx'

          it may also be a single number specifying the time window
          around the peak for which to plot EIC data 

     col: color to use for plotting extracted ion chromatograms. if
          missing and 'y' is specified, colors are taken from
          'unclass(sampclass(y))' and the default palette

          if it is the same length as the number groups in the
          'xcmsEIC' object, then 'sampleidx' is used to subset it.
          otherwise, it is repeated over the length of 'sampleidx' 

 legtext: text to use for legend. if 'NULL' and 'y' is specified,
          legend text is taken from the sample class information found
          in the 'xcmsSet' 

 peakint: logical, plot integrated peak area with darkened lines
          (requires that 'y' also be specified) 

   sleep: seconds to pause between plotting EICs

_M_e_t_h_o_d_s:

     _x = "_x_c_m_s_E_I_C" 'plot(x, y, groupidx = groupnames(x), sampleidx =
          sampnames(x),  rtrange = x@rtrange, col = rep(1,
          length(sampleidx)),  legtext = NULL, peakint = TRUE, sleep =
          0)'

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

     'xcmsEIC-class', 'png', 'pdf', 'postscript',

