threePanelPlot             package:prada             R Documentation

_V_i_s_u_a_l_i_z_e _c_y_t_o_m_e_t_r_y _d_a_t_a

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

     Function to visualize multivariate (cytometry) data in three
     two-dimensional plots.

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

     threePanelPlot(data, x.panels = c(1, 4, 5), y.panels = c(2, 3, 6),
                    tot.width = 15, tot.height = 5.4, maxcells = 20000,
                    limits = c(0, 1023), remove.extremes = TRUE,
                    plotTitle = "Three-Panel Plot", use.smoothScatter = TRUE,
                    palette = colorRampPalette(brewer.pal(9, "Blues")),
                    new.device = TRUE, verbose = TRUE,
                    addPoints = NULL, addCol = "red", ...)

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

    data: data matrix to visualize

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

tot.width: width of a new device to open, see argument 'new.device'

tot.height: height of a new device to open, see argument 'new.device'

maxcells: maximum number of observations (cells) for plotting; higher
          numbers reduce performance

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

remove.extremes: logical; are extreme values (equal to theoretical
          'limits') to be removed before plotting

plotTitle: title for the plot

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

 palette: if 'smoothScatter' is used, which colour palette is it to use

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

addPoints: should special points be marked after plotting the data; is
          expected to be a subser of argument 'data' with the same
          number of columns (=variables); if 'NULL' no points are
          marked

  addCol: in which colour are the points in 'addPoints' to be marked

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

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

     no value is returned; the function is called to produce three
     plots

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

     Joern Toedling toedling@ebi.ac.uk

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

     'plot.default'

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

        # generate some data:
        toyData <- cbind(matrix(pmax(0,pmin(runif(3000)+rnorm(3000),4)),ncol=3),
                         matrix(pmax(0,pmin(rnorm(3000,2,1),4)),ncol=3))
        colnames(toyData) <- paste("Var",1:6,sep="")
        toyQuantiles <- apply(toyData,2,quantile,probs=c(0.25,0.5,0.75))

        # plot it and mark the quantiles:
        threePanelPlot(toyData,addPoints=toyQuantiles,
                       addCol=c("orange","red","purple"),limits=c(0,4),pch=20)

