Method implementing Lattice ECDF plots for flow data

Share:

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
prepanel.ecdfplot.flowset(x, frames, channel, f.value, ...)

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

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

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.

frames

environment containing frame-specific data

channel

expression involving names of columns in the data

f.value

determines the number of points used in the plot ecdfplot for details.

ref

logical; whether to add reference lines at 0 and 1

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

data

a flowSet object that serves as a source of data

xlab

Labels for data axes, with suitable defaults taken from the formula

panel,prepanel

the panel and prepanel functions.

type

type of rendering; by default lines are drawn

as.table

logical; whether to draw panels from top left

...

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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))