densityplot: One-dimensional density/histogram plots for flow data
In flowViz: Visualization for flow cytometry

Description Usage Arguments Details Examples

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.

## 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,ncdfFlowSet'
densityplot(x, data, ...)

## S4 method for signature 'formula,ncdfFlowList'
densityplot(x, data, ...)

## S4 method for signature 'formula,flowSet'
histogram(x, data, plotType, ...)

## S4 method for signature 'formula,flowFrame'
histogram(x, data, ...)

## S4 method for signature 'formula,ncdfFlowSet'
histogram(x, data, ...)

## S4 method for signature 'formula,ncdfFlowList'
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.
`data`	A flow data object that serves as a source of data, either a `flowFrame` or `flowSet`
`...`	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
`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`	Arguments to control statistics that is associated with `filter` to be plotted. see xyplot for details.
`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 names
`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 `par.settings` for customization of a single call or `flowViz.par.set` for customization of session-wide defaults.
`overlay`	see help(xyplot).

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).

library(flowCore)
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)