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',

