`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.```
## S3 method for class '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, ...)

## S3 method for class 'formula,flowFrame':
densityplot(x, data, overlay = NULL, ...)

## S3 method for class 'formula,view':
densityplot(x, data, ...)

## S3 method for class 'formula,flowSet':
histogram(x, data, plotType, ...)

## S3 method for class 'formula,flowFrame':
histogram(x, data, ...)

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.frames

An environment containing frame-specific data.

overlap

The amount of overlap between stacked density plots. This
argument is ignored for the

`flowFrame`

method.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.

`darg`

gets passed on to `density`

.channel

The name of the currently plotted flow parameter.

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).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`

, `fill`

,
`lwd`

, `alpha`

and `lty`

. See
`flowViz.par.set`

for details.groups

Use identical colors for grouping. The value of the argument
is expected to be a phenotypic variable in the

`flowSet`

, or a factor.refline

Logical. Add one ore more vertical reference lines to the
plot. This argument is directly passed to

`panel.abline`

.margin

Either Logical value 'FALSE' or Numeric valuein

`[0,1]`

.
When 'FALSE', it doesn't do anything to the margin events. When Numeric
value, it indicates margin events by horizontal bars. The value of
`margin`

is interpreted as the proportion of events on the margin over
which the bars are added. E.g., a value of `0,5`

means to indicate
margin events if there are more than `0.5`

times the total number of
events. `1`

means to ignore margin events completetly. For `0`

bars are added even if there is only a single margin event.stats,pos,digits,abs

fitGate

A

`logical`

scalar indicating whether to display the
gate as fitted 1d density gate region or simply display the gate boundaries
using vertical lines. The latter would be helpful to display the gate when
the gated density region is too small to see.checkName

A

`logical`

scalar indicating whether to validity
check the channel name. Default is TRUE, which consider '(' as invalid
character in channel namesplotType

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

`par.settings`

for
customization of a single call or `flowViz.par.set`

for customization
of session-wide defaults.overlay

see help(xyplot).

...

More arguments, usually passed on to the underlying lattice
methods.

- channels A character vector of parameters that are supposed to be
plotted when the formula in
`x`

is of structure`factor ~ .`

. - xlab: Label for data x axis, with suitable defaults taken from the formula
- prepanel: The prepanel function. See
`xyplot`

- panel: the panel function. See
`xyplot`

- axis: axis function passed to lattice, default is
`axis.grid`

- ... : other arguments passed to panel.densityplot.flowset.stack or panel.histogram.flowframe

library(flowStats) 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")) #display the gate by its boundaries with statistics densityplot(~ `FSC-H`, GvHD[1:2], filter=curv1Filter("FSC-H"),fitGate=FALSE,stats=TRUE) ## plot a single flowFrame densityplot(~ `SSC-H`, GvHD[[1]], margin=FALSE) ## plot histogram histogram(~ `SSC-H`, GvHD[[1]]) #default type is 'density' #change the type to 'count' and adjust breaks histogram(~ `SSC-H`, GvHD[[1]], margin=FALSE, type = "count", breaks = 50)