ecdfplot: Method implementing Lattice ECDF plots for flow data

In flowViz: Visualization for flow cytometry

Description

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

Usage

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.
...	more arguments, usually passed on to the underlying lattice methods and the panel function.
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

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

library(flowCore)
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))

flowViz documentation built on Nov. 8, 2020, 7:53 p.m.