plotEIC-methods             package:xcms             R Documentation

_P_l_o_t _a _l_i_s_t _o_f _E_I_C_s _f_o_r _e_a_c_h _s_a_m_p_l_e

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

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

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

  object: the 'xcmsSet' object

    eics: list of EIC matricies as produced by 'link{getEIC}' 

peakrange: matrix with named columns: 'mzmin', 'mzmax', 'rtmin', and
          'rtmax' 

    nums: integer vector of indecies of EICs to plot 

classlabel: factor with class labels for each EIC matrix in the list 

peakindex: integer vector with indecies to the rows of the 'xcmsSet'
          'group' matrix corresponding to the rows of the 'peakrange'
          matrix 

filebase: base file name under which to save the numbered EICs, no
          image files are saved if missing 

      wh: integer vector of length two with pixel width and height of
          the output PNG images 

   sleep: seconds to pause between plotting EICs, only useful if
          'filebase' is missing and the plots are interactively output 

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

     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" 'plotEIC(object, eics, peakrange, nums =
          seq(length = nrow(peakrange)),  classlabel =
          sampclass(object), peakindex = NULL, filebase = character(),
          wh = c(640,480),  sleep = 0)'

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

     'xcmsSet-class'

