densityplot             package:flowViz             R Documentation

_O_n_e-_d_i_m_e_n_s_i_o_n_a_l _d_e_n_s_i_t_y _p_l_o_t_s _f_o_r _f_l_o_w _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     So far, density plots are only implemented for 'flowSet'. The idea
     is to horizontally stack plots of density estimates for all frames
     in the 'flowSet' for one or several flow parameters. In the latter
     case, each parameter will be plotted in a separate panel, i.e., we
     implicitely condition on parameters.

_U_s_a_g_e:

     ## method for 'flowSet' objects
     ## S4 method for signature 'formula, flowSet':
     densityplot(
         x,
         data, 
         xlab,
         as.table=TRUE,
         overlap=0.3,
         prepanel=prepanel.densityplot.flowset,
         panel = panel.densityplot.flowset,
         filter=NULL,
         scales=list(y=list(draw=F)),
         channels,
         ...)

     prepanel.densityplot.flowset(
         x,
         y,
         darg=list(n=50, na.rm=TRUE),
         frames, 
         overlap=0.3,
         subscripts,
         ...,
         which.channel)

     panel.densityplot.flowset(
         x,
         y,
         darg=list(n=50, na.rm=TRUE),
         frames,
         channel,
         overlap = 0.3,
         channel.name,
         filter=NULL,
         fill=superpose.polygon$col,
         lty=superpose.polygon$lty,
         lwd=superpose.polygon$lwd,
         alpha=superpose.polygon$alpha,
         col=superpose.polygon$border,
         groups=NULL,
         refline=NULL,
         gpar,
         ...)


     ## methods for various workflow objects
     ## S4 method for signature 'formula, view':
     densityplot(
         x,
         data,
         ...)

     ## S4 method for signature 'view, missing':
     densityplot(
         x,
         data,
         channels,
         ...)

_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. The structure of the
          formula is 'factor ~ parameter', where 'factor' can be any of
          the phenotypic factors in the 'phenoData' slot or an
          appropriate factor object and 'parameter' is a flow
          parameter. Panels for multiple parameters are drawn if the
          formula structure is similar to 'factor ~ parameter1 +
          parameter2', and 'factor' can be missing, in which case the
          sample names are used as y-variable. To facilitate
          programatic access, the formula can be of special structure
          'factor ~ .', in which case the optional 'channel' argument
          is considered for parameter selection. For the workflow
          methods, 'x' can also be one of the several workflow objects. 

    data: A 'flowSet' object that serves as a source of data, either a
          'flowFrame' or 'flowSet', or one of the several workflow
          objects. 

    xlab: Label for data x axis, with suitable defaults taken from the
          formula 

as.table, scales, darg: These arguments are passed unchanged to the
          corresponding methods in lattice, and are listed here only
          because they provide different defaults.  See documentation
          for the original methods for details. 'darg' gets passed on
          to 'density'. 

 overlap: The amount of overlap between stacked density plots 

prepanel: The prepanel function.  See 'xyplot' 

   panel: the panel function.  See 'xyplot' 

  filter: A 'filter', 'filterResult' or 'filterResultList' object or a
          list of such objects of the same length as the 'flowSet'. If
          applicable, the gate region will be superiposed on the
          density curves using color shading. The software will figure
          out whether the 'filter' needs to be evaluated in order to be
          plotted (in which case providing a 'filterResult' can speed
          things up considerably). 

channels: A character vector of parameters that are supposed to be
          plotted when the formula in 'x' is of structure 'factor ~ .'. 

subscripts, which.channel, channel.name, y: Internal indices necessary
          to map panels to parameters. 

  frames: An environment containing frame-specific data. 

 channel: The name of the currently plotted flow parameter. 

col, fill, lty, lwd, alpha: Graphical parameters. These mostly exist
          for conveniance and much more control is available throught
          the 'lattice'-like 'par.setting' and 'flowViz.par.set'
          customization. The relevant parameter category for density
          plots is 'gate.density' with available parameters 'col,
          \code{fill}, \code{lwd} \code{alpha} and \code{lty}'. See
          'flowViz.par.set' for details.

  groups: Use identical colors for grouping. The value of the argument
          is expected to be a phenotypic variable in the 'flowSet'. 

 refline: Add one ore more vertical reference lines to the plot. This
          argument is directly passed to 'panel.abline'. 

    gpar: A list of graphical parameters that are passed down to the
          low level panel functions. This is for internal use only. The
          public user interface to set graphical parameters is either
          'par.settings' for customization of a single call or
          'flowViz.par.set' for customization of session-wide defaults. 

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

_D_e_t_a_i_l_s:

     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 (Trellis docs
     would also work for the fundamentals).

_M_e_t_h_o_d_s:



     _d_e_n_s_i_t_y_p_l_o_t 'signature(x = "formula", data = "flowSet")': Creates
          density plots for one or several channels, with samples
          stacked according to a 'phenoData' variable. Colors are used
          to indicate common values of this covariate across panels.
          Filters can be added as the optional 'filter' arguments. See
          'xyplot' for details. 

     _d_e_n_s_i_t_y_p_l_o_t 'signature(x = "formula", data = "view")': A method to
          create density plots for workspace 'view' objects. This still
          allows for some level of customization, but most defaults
          will be set depending on the input object. 

     _d_e_n_s_i_t_y_p_l_o_t 'signature(x = "view", data = "missing")': The default
          method for view objects. All defaults will be set. 


_E_x_a_m_p_l_e_s:

     data(GvHD)
     GvHD <- GvHD[pData(GvHD)$Patient %in% 6:7]

     densityplot(~ `FSC-H`, GvHD)

     densityplot(~ `FSC-H` + `SSC-H`, GvHD)

     densityplot(~ ., GvHD[1:3])

     ## include a filter
     densityplot(~ `FSC-H`, GvHD, filter=curv1Filter("FSC-H"))

