multiecdf {geneplotter}R Documentation

Multiple empirical cumulative distribution functions (ecdf) and densities

Description

Plot multiple empirical cumulative distribution functions (ecdf) and densities with user interface similar to that of boxplot.

Usage

multiecdf(x, ...)
## S3 method for class 'formula':
multiecdf(formula, data = NULL, xlab, na.action = NULL, ...)
## S3 method for class 'matrix':
multiecdf(x, xlab, ...) 
## S3 method for class 'list':
multiecdf(x,
          xlim,
          col = brewer.pal(9, "Set1"),
          main = "ecdf",
          xlab,
          do.points = FALSE,
          subsample = 1000L,
          legend = list(
            x = "right",
            legend = if(is.null(names(x))) paste(seq(along=x)) else names(x),
            fill = col),
          ...)

multidensity(x, ...)
## S3 method for class 'formula':
multidensity(formula, data = NULL, xlab, na.action = NULL, ...)
## S3 method for class 'matrix':
multidensity(x, xlab, ...) 
## S3 method for class 'list':
multidensity(x,
             bw = "nrd0",
             xlim,
             ylim,
             col  = brewer.pal(9, "Set1"),
             main = if(length(x)==1) "density" else "densities",
             xlab,
             lty  = 1L,
             legend = list(
               x = "topright",
               legend = if(is.null(names(x))) paste(seq(along=x)) else names(x),
               fill = col),
             ...)

Arguments

formula a formula, such as y ~ grp, where y is a numeric vector of data values to be split into groups according to the grouping variable grp (usually a factor).
data a data.frame (or list) from which the variables in formula should be taken.
na.action a function which indicates what should happen when the data contain NAs. The default is to ignore missing values in either the response or the group.
x a list of numeric vectors.
bw the smoothing bandwidth, see the manual page for density. If bw is a character string specifying a rule to choose the bandwidth, this rule is applied to x[[1]] and then the same numerical value of bw is used throughout.
xlim Range of the x axis. If missing, the data range is used.
ylim Range of the y axis. If missing, the range of the density estimates is used.
col, lty Line colors and line type.
main Plot title.
xlab x-axis label.
do.points logical; if TRUE, also draw points at the knot locations.
subsample numeric or logical of length 1. If numeric, and larger than 0, subsamples of that size are used to compute and plot the ecdf for those elements of x with more than that number of observations. If logical and TRUE, a value of 1000 is used for the subsample size.
legend a list of arguments that is passed to the function legend.
... Further arguments that get passed on to the plot functions.

Details

The usefulness of multidensity can vary, depending on the data and because of smoothing artifacts. multiecdf will in many cases be preferable.

Value

For the multidensity functions, a list of density objects.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

See Also

boxplot, ecdf, density

Examples

  words = strsplit(packageDescription("geneplotter")$Description, " ")[[1]]
  factr = factor(sample(words, 2000, replace = TRUE))
  x = rnorm(length(factr), mean=as.integer(factr))
  
  multiecdf(x ~ factr)
  multidensity(x ~ factr)

[Package geneplotter version 1.22.0 Index]