flowPlot               package:flowViz               R Documentation

_S_t_a_n_d_a_r_d _P_l_o_t_s _f_o_r _F_l_o_w _C_y_t_o_m_e_t_r_y _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     A method that makes standard plots from a 'flowFrame'. The user
     may also provide various 'filter' or 'filterResult' arguments to
     customize the plot.

_U_s_a_g_e:

     flowPlot(x, ...)

     ## S4 method for signature 'flowFrame':
     flowPlot(x, child, filter = NULL,
              plotParameters = c("FSC-H","SSC-H"),
              logx = FALSE, logy = FALSE,
              parent, colParent="Grey", colChild="Blue",
              showFilter = TRUE, gate.fill = "transparent",
              gate.border = "black", xlab, ylab, xlim, ylim,
              ...)

_A_r_g_u_m_e_n_t_s:

       x: An object of class 'flowFrame' that contains the data to be
          plotted.

   child: An optional argument of class 'filterResult' that specifies a
          subset of the data that are included in the 'filterResult'

  filter: 

plotParameters: 

    logx: 

    logy: 

  parent: 

colParent: 

colChild: 

showFilter: 

gate.fill: 

gate.border: 

    xlab: 

    ylab: 

    xlim: 

    ylim: 

     ...: 

_D_e_t_a_i_l_s:

     The plot that is most commonly used in flow cytometry data
     analysis is usuall called a "dot plot". In common statistical
     language, we would call this a scatter plot. The basic idea is a
     2-dimensional plot that shows the location of every cell in regard
     to the measurements made on it, for example, forward scatter vs
     side scatter. Most applications will, in addition to the data,
     want to show information about one or more filters (gates). Since
     there can be a very large number of cells in a sample, it is
     common to show a smoothed version of the data that doesn't involve
     registering every point on the graph.

_A_u_t_h_o_r(_s):

     P. Haaland

_S_e_e _A_l_s_o:

     'flowCore'

_E_x_a_m_p_l_e_s:

     data(GvHD)
     flowPlot(GvHD[["s5a01"]])
     flowPlot(transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD[["s5a01"]])

