plotPeaks-methods            package:xcms            R Documentation

_P_l_o_t _a _g_r_i_d _o_f _a _l_a_r_g_e _n_u_m_b_e_r _o_f _p_e_a_k_s

_D_e_s_c_r_i_p_t_i_o_n:

     Plot extracted ion chromatograms for many peaks simultaneously, 
     indicating peak integration start and end points with vertical
     grey lines.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsRaw' object

   peaks: matrix with peak information as produced by 'findPeaks' 

    figs: two-element vector describing the number of rows and the
          number of columns of peaks to plot, if missing then an
          approximately square grid that will fit the number of peaks
          supplied 

   width: width of chromatogram retention time to plot for each peak 

_D_e_t_a_i_l_s:

     This function is intended to help graphically analyze the results
     of peak picking. It can help estimate the number of false
     positives and improper integration start and end points. Its
     output is very compact and tries to waste as little space as
     possible. Each plot is labeled with rounded m/z and retention time
     separated by a space.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" 'plotPeaks(object, peaks, figs, width = 200)'


_S_e_e _A_l_s_o:

     'xcmsRaw-class', 'findPeaks', 'split.screen'

