plotvar.FCS {rflowcyt}R Documentation

Making Univariate/Bivariate plots of the column variables of a FCS object

Description

A univariate histogram or scatterplot will be made for a single column variable specified from the data of the FCS object, or a bivariate scatterplot or contour-image scatter plot will be shown for any two variables specified in the FCS object.

Usage

plotvar.FCS(x, varpos, type = c("uni", "bi"), 
           plotType = c("hist", "ContourScatterPlot", "plot"),
           names.var = NULL, title.pl = "",
           xlimit = NULL, ylimit = NULL, plot.freq = TRUE,
           color.hist.plot = "white", CSPlot = TRUE,
           hexbin.CSPlot=TRUE,
           hexbin.style.CSPlot=c("colorscale", "lattice", "centroids",
                "nested.lattice", "nested.centroids"),
           n.hexbins.CSPlot=100,
           x.grid.CSPlot = seq(0, 1025, by = 25),
           y.grid.CSPlot = seq(0, 1025, by = 25),
           image.col.CSPlot = heat.colors(2),
           numlev.CSPlot = 25,
           xaxt="s", yaxt="s",
           MY.DEBUG = FALSE,...)

Arguments

x FCS object
varpos the numerical column variable position of the data of the FCS object
type character string specifying the type of plot; either "uni" for univariate or "bi" for bivariate; currently this option need not be specified because of automatic detection within the function
plotType the type of plot to be used; either plot, hist, ContourScatterPlot; currently this option need not be specified because of automatic detection within the function; a univariate histogram plot is default when varpos is a single numeric value, and a default contour-image scatter plot with hexagonal binning or rectangular binning is displayed for a bivariate plot.
names.var (optional) character string or vector of characte strings of the variable or variables to be plotted; default is NULL and will be changed to the names specified in the data of the FCS object
title.pl character string of the plot title (main)
xlimit numerical vector of the range of the x variable (horizontal axis)
ylimit numerical vector of the range of the y variable (vertical axis)
plot.freq boolean; if TRUE, then the frequencies instead of the relative frequencies are plotted (only if plotType=hist)
color.hist.plot character string or numerical value indicating the color of the histogram plot
CSPlot a boolean of whether or not this is a ContourScatterPlot; if FALSE then an ordinary scatterplot is produced
hexbin.CSPlot boolean; if TRUE then the grid cells/compartments are hexagons; otherwise the grid cells are rectangular; default value is TRUE
hexbin.style.CSPlot the style of hexbin plot; default is "colorscale" (for ContourScatterPlot hexagonal binning ONLY!)
n.hexbins.CSPlot number of xbins for hexagon binning; default is 100 (for ContourScatterPlot hexagonal binning ONLY!)
x.grid.CSPlot a numeical sequence denoting the grid marks for the x coordinate (for ContourScatterPlot rectanglar binning ONLY!)
y.grid.CSPlot a numerical sequence denoting the grid marks for the y coordinate (for ContourScatterPlot rectanglar binning ONLY!)
image.col.CSPlot a color map for the image (for ContourScatterPlot rectanglar binning ONLY!)
numlev.CSPlot number of levels for the contours in a ContourScatterPlot (for ContourScatterPlot rectanglar binning ONLY!)
xaxt if "s", then the x-axis is plotted, if "n" then there is no x-axis plotted (for ContourScatterPlot rectanglar binning ONLY!)
yaxt if "s", then the y-axis is plotted, if "n" then there is no y-axis plotted (for ContourScatterPlot rectanglar binning ONLY!)
MY.DEBUG boolean; if TRUE then the variable check statements are printed; default is FALSE
... plot options (for histograms and ContourScatterPlot hexagonal binning) or contour options for ContourScatterPlot rectangular binning

Details

Other options from the functions plot, hist, ContourScatterPlot may be used in the signature of this function to define the plot further.

Value

Either a univariate or a bivariate plot of the specified variable(s) of the FCS object. A hist plot will output the breaks and bins of the histogram.

WARNING

Please read the warning for ContourScatterPlot.

Note

For a description of colors please look up colors, palette, and heat.colors

Author(s)

A.J. Rossini and J.Y. Wan

See Also

ContourScatterPlot, plot, hist

Examples


  ### to identify all the colors available on your system
  colors()
  if (interactive()) {
    if (require(rfcdmin)) {

      if (!is.element("unst.1829", objects())) {
        ## obtaining the FCS objects from VRC data
        data(VRCmin)
      }

      ## univariate plot
      plotvar.FCS(unst.1829, varpos=1)

      ## bivariate plot :hexagonal binning
      plotvar.FCS(unst.1829, varpos=c(1,2))

      ## bivariate plot :rectangonal binning
      plotvar.FCS(unst.1829, varpos=c(1,2), hexbin.CSPlot=FALSE)
    }
  }


[Package rflowcyt version 1.10.1 Index]