splom                package:flowViz                R Documentation

_M_e_t_h_o_d _i_m_p_l_e_m_e_n_t_i_n_g _L_a_t_t_i_c_e _s_c_a_t_t_e_r _p_l_o_t _m_a_t_r_i_c_e_s _f_o_r _f_l_o_w _d_a_t_a.

_D_e_s_c_r_i_p_t_i_o_n:

     This function create Trellis scatter plots matrices (splom) from
     flow cytometry data.

_U_s_a_g_e:

     ## S4 method for signature 'flowFrame, missing':
     splom(
         x,
         data, 
         pscales,
         time,
         exclude.time=TRUE,
         names=FALSE,
         ...)

     panel.splom.flowframe(
         x,
         frame,
         ...)

_A_r_g_u_m_e_n_t_s:

       x: A formula describing the structure of the plot and the
          variables to be used in the display. 

data, frame: A 'flowFrame' object that serves as the source of data. 

 pscales: This arguments is passed unchanged to the corresponding
          methods in lattice, and is listed here only because it
          provides a different default.  See documentation for the
          original methods for details. 

    time: A character string giving the name of the data column
          recording time. If not provided, we try to guess from the
          available parameters. 

exclude.time: Logical, specifying whether to exclude the time variable
          from a scatter plot matrix. Defaults to 'TRUE'. 

   names: Logical specifying wether gate names should be added to the
          plot. Currently, this feature is not supported for splom
          plots. 

     ...: More arguments, usually passed on to the underlying lattice
          methods. 

_D_e_t_a_i_l_s:

     The function draws a scatter plot matrix of the data for each flow
     parameter in a 'flowFrame'. For the most, one can think about this
     as a rectangular arrangement of separate 'xyplots', and most of
     that functionality is also available here. To be more precise, the
     function repeatedly calls 'panel.xyplot.flowframe' to do the
     actual plotting. Please see its documentation for details.

_M_e_t_h_o_d_s:



     _s_p_l_o_m 'signature(x = "flowFrame", data = "missing")': Creates a
          scatter plot matrix for a whole 'flowFrame'. The actual
          plotting is done by 'panel.xyplot.flowframe', so most
          additional arguments from the regular 'xyplot' are also valid
          here. 


_A_u_t_h_o_r(_s):

     F. Hahne, D. Sarkar

_S_e_e _A_l_s_o:

     Not all standard lattice arguments will have the intended effect,
     but many should.  For a fuller description of possible arguments
     and their effects, consult documentation on lattice.

_E_x_a_m_p_l_e_s:

     data(GvHD)

     tf <- transformList(colnames(GvHD)[3:7], asinh)
     dat <- tf %on% GvHD[[3]]

     ## scatter plot matrix of individual flowFrames
     lattice.options(panel.error=NULL)
     splom(dat)

     splom(dat[,1:3], smooth = FALSE)

     ## displaying filters
     rg <- rectangleGate("FSC-H"=c(200,400), "SSC-H"=c(300,700),
     "FL1-H"=c(2,4), "FL2-A"=c(4,7))
     splom(dat, filter=rg)

     splom(dat, filter=rectangleGate("FSC-H"=c(400,800)))

     splom(dat[,1:4], smooth = FALSE, filter=norm2Filter("FSC-H", "SSC-H", scale=1.5))

