plotGate                package:prada                R Documentation

_V_i_s_u_a_l_i_z_e _O_b_s_e_r_v_a_t_i_o_n_s _w_i_t_h_i_n _d_e_f_i_n_e_d _G_a_t_e_s

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

     This functions visualize which observations are included in gates
     defined by the functions 'gate.cytoFrame', 'gate.cytoSet', and
     'gate.matrix'. The make use of the visualization function
     'threePanelPlot' .

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

     plot.cytoFrameGate(x, y, x.panels = c(1, 4, 5), y.panels = c(2, 3, 6),
                        use.smoothScatter = TRUE, limits = c(0, 1023),
                        plotTitle = "Gated Data", gate.colour = "red",
                        new.device = TRUE, verbose = TRUE, ...)

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

       x: gate resulting, e.g.,  from function 'gate.cytoFrame'; thus
          'x' is of class 'cytoFrameGate' or similar

       y: the original data used to derive gate 'x', thus either a
          'cytoFrame', 'cytoSet' or 'matrix'

x.panels: which variables (columns) are to be plotted at the x-axis of
          the three variables

y.panels: which variables (columns) are to be plotted at the y-axis of
          the three variables

use.smoothScatter: logical, should the function 'smoothScatter' be
          employed for plotting the data (plots data densities rather
          than individual points)

  limits: minimum and maximum value (theoretically) observed in the
          data; e.g., with 10-channel digitized data it is c(0,1023)

plotTitle: title for the plot

gate.colour: which colour to use for observations within the gate 'x'

new.device: logical; should a new device be opened for the three plots;
          if 'FALSE' the three plots will be plotted to the currently
          active device

 verbose: logical; do you want extended output to STDOUT

     ...: further arguments passed on to 'plot.default'

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

     No value is returned. These functions are called for producing the
     three plots.

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

     Joern Toedling toedling@ebi.ac.uk

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

     'gate.cytoFrame','threePanelPlot'

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

        # see the example in function 'gate.cytoFrame'

