plotvar.FCS {rflowcyt} | R Documentation |
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.
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,...)
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 |
Other options from the functions plot
,
hist
, ContourScatterPlot
may be
used in the signature of this function to define the plot further.
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.
Please read the warning for ContourScatterPlot
.
For a description of colors please look up colors
,
palette
, and heat.colors
A.J. Rossini and J.Y. Wan
ContourScatterPlot
,
plot
, hist
### 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) } }