ecdfplot {flowViz}R Documentation

Method implementing Lattice ECDF plots for flow data

Description

This function creates Trellis displays of Empirical Cumulative Distribution Functions from flow cytometry data using a formula interface.

Usage


## methods for 'flowSet' objects

## S4 method for signature 'formula, flowSet':
ecdfplot(x, data, xlab, ylab,
         f.value = function(n) ppoints(ceiling(sqrt(n))),
         type = "l", as.table = TRUE,
         ...)

prepanel.ecdfplot.flowset(x, frames, channel, 
                          f.value, ...)
panel.ecdfplot.flowset(x, frames, channel,
                       f.value, ref = TRUE,
                       groups = NULL, subscripts,
                       col, col.points, pch, cex, 
                       alpha, col.line, lty, lwd, ...)

Arguments

x a formula describing the structure of the plot and the variables to be used in the display. For the prepanel and panel functions, a vector of names for the flow frames to be used in the panel.
data a flowSet object that serves as a source of data
xlab, ylab Labels for data axes, with suitable defaults taken from the formula
f.value determines the number of points used in the plot ecdfplot for details.
type type of rendering; by default lines are drawn
as.table logical; whether to draw panels from top left
ref logical; whether to add reference lines at 0 and 1
frames environment containing frame-specific data
channel expression involving names of columns in the data
groups, subscripts grouping variable, if specified, and subscripts indexing which frames are being used in the panel. See xyplot for details.
col, col.points, pch, cex, alpha, col.line, lty, lwd vector of graphical parameters that are replicated for each group
... more arguments, usually passed on to the underlying lattice methods and the panel function.

Methods

ecdfplot
signature(x = "formula", data = "flowSet"): plote empirical CDF for a given channel, with one or more samples per panel

See Also

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.

Examples


data(GvHD)

ecdfplot(~ `FSC-H` | Patient, GvHD, f.value = ppoints(100))

ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD,
         strip = strip.custom(strip.names = TRUE),
         ref = FALSE)

ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD, groups = Visit,
         strip = strip.custom(strip.names = TRUE),
         ref = FALSE, auto.key = list(columns = 4))


[Package flowViz version 1.6.2 Index]