Onedimensional density/histogram plots for flow data
Description
For flowSets
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 implicitly condition
on parameters.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26  ## S4 method for signature 'formula,flowSet'
densityplot(x, data, ...)
prepanel.densityplot.flowset.stack(x, y, frames, overlap = 0.3, subscripts,
..., which.channel)
panel.densityplot.flowset.stack(x, y, darg = list(n = 50, na.rm = TRUE),
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, groups = NULL, refline = NULL,
margin = 0.005, stats = FALSE, pos = 0.5, digits = 2, abs = FALSE,
fitGate = TRUE, checkName = TRUE, plotType = "densityplot",
hist.type = "density", breaks = "Sturges", gp, ...)
## S4 method for signature 'formula,flowFrame'
densityplot(x, data, overlay = NULL, ...)
## S4 method for signature 'formula,view'
densityplot(x, data, ...)
## S4 method for signature 'formula,flowSet'
histogram(x, data, plotType, ...)
## S4 method for signature 'formula,flowFrame'
histogram(x, data, ...)

Arguments
x 
A formula describing the structure of the plot and the variables to
be used in the display. The structure of the formula is 
data 
A flow data object that serves as a source of data, either a

frames 
An environment containing framespecific data. 
overlap 
The amount of overlap between stacked density plots. This
argument is ignored for the 
subscripts,which.channel,channel.name,y 
Internal indices necessary to map panels to parameters. 
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.

channel 
The name of the currently plotted flow parameter. 
filter 
A 
col,fill,lty,lwd,alpha 
Graphical parameters. These mostly exist for
conveniance and much more control is available throught the

groups 
Use identical colors for grouping. The value of the argument
is expected to be a phenotypic variable in the 
refline 
Logical. Add one ore more vertical reference lines to the
plot. This argument is directly passed to

margin 
Either Logical value 'FALSE' or Numeric valuein 
stats,pos,digits,abs 
Arguments to control statistics that is
associated with 
fitGate 
A 
checkName 
A 
plotType 
either 'densityplot' or 'histogram' 
hist.type 
see 'type' argument in 'help(panel.histogram)' 
breaks 
see 'help(hist)' 
gp 
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 
overlay 
see help(xyplot). 
... 
More arguments, usually passed on to the underlying lattice methods.

Details
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).
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23  library(flowStats)
data(GvHD)
GvHD < GvHD[pData(GvHD)$Patient %in% 6:7]
densityplot(~ `FSCH`, GvHD)
densityplot(~ `FSCH` + `SSCH`, GvHD)
densityplot(~ ., GvHD[1:3])
## include a filter
densityplot(~ `FSCH`, GvHD, filter=curv1Filter("FSCH"))
#display the gate by its boundaries with statistics
densityplot(~ `FSCH`, GvHD[1:2], filter=curv1Filter("FSCH"),fitGate=FALSE,stats=TRUE)
## plot a single flowFrame
densityplot(~ `SSCH`, GvHD[[1]], margin=FALSE)
## plot histogram
histogram(~ `SSCH`, GvHD[[1]]) #default type is 'density'
#change the type to 'count' and adjust breaks
histogram(~ `SSCH`, GvHD[[1]], margin=FALSE, type = "count", breaks = 50)

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