densityplot {flowViz} | R Documentation |
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.
## 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), frames, overlap=0.3, subscripts, ..., which.channel) panel.densityplot.flowset( x, y, darg=list(n=50), 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, 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, ...)
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. |
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. |
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).
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. 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. signature(x = "view", data = "missing")
:
The default method for view objects. All defaults will be set.
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"))