flowViz (version 1.30.1)

densityplot: One-dimensional density 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 implicitely condition on parameters.

Usage

## method for 'flowSet' objects
"densityplot"( x, data, ...)
## method for 'flowFrame' objects
"densityplot"( x, data,  ...)
prepanel.densityplot.flowset( x, y, frames,  overlap=0.3, subscripts, ..., which.channel)
panel.densityplot.flowset( 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 ,gp, ...)

## methods for various workflow objects
"densityplot"( x, data, ...)

"densityplot"( x, data, channels, ...)

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 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, or one of the several workflow objects.

overlap

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

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).

groups

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

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.

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.

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.

refline

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

margin

Numeric in [0,1]. Indicate 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

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.

...

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

• 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

Methods

densityplot

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.

densityplot

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.

densityplot

signature(x = "view", data = "missing"): The default method for view objects. All defaults will be set.

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

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)