splom {flowViz} | R Documentation |
This function create Trellis scatter plots matrices (splom) from flow cytometry data.
## S4 method for signature 'flowFrame, missing': splom( x, data, pscales, time, exclude.time=TRUE, names=FALSE, ...) panel.splom.flowframe( x, frame, ...)
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. |
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.
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.
F. Hahne, D. Sarkar
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.
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))