pplot: pplot

In raredd/rawr: rawr miscellaneous

pplot

Description

A paired plot for continuous data. Draws a dot plot with points jittered to the left and right about the group position. Jittering is done with beeswarm; however, the original data values are used instead of using the slight adjustments made by beeswarm. Additionally, a two-sample wilcox.test test is performed on each pair by default, but the test and assumptions may be controlled using test and args.test arguments, respectively; see examples.

Usage

pplot(x, ...)

## S3 method for class 'formula'
pplot(formula, data, ...)

## Default S3 method:
pplot(
  x,
  at = seq_along(x),
  pad = 0.05,
  test = wilcox.test,
  args.test = list(),
  col = 1:2,
  pch = par("pch"),
  cex = par("cex"),
  args.beeswarm = list(),
  names,
  quantiles = NULL,
  pch.quantiles = rep_len(16L, length(quantiles)),
  xlab = NULL,
  ylab = NULL,
  legend.text = NULL,
  ...
)

Arguments

x	for the default method, a list of groups each having a list of length 2 of data values
...	for the formula method, named arguments to be passed to the default method for the default method, additional arguments passed to tplot or graphical parameters passed to par
formula	a formula, such as y ~ group1 + group2, where y is a numeric vector of data values to be split into n groups (group1), each group split into at most two groups (group2)
data	a data frame (or list) from which the variables in formula should be taken
at	the x-axis group positions
pad	the padding between at for each group and the points
test	logical or function; if TRUE, a wilcox.test p-value is added for each group alternatively, a function (or function name as a character string) can be used, e.g., test = t.test or function(x, y) t.test(x, y); note that if test is a function, it must have at least two arguments with the two groups of data; see examples
args.test	a named list of arguments passed to test
col, pch, cex	color, plotting character, and character expansion vectors, each may be length 1, 2, or total number of groups to be plotted, recycled as needed
args.beeswarm	a named list of arguments passed to beeswarm to override defaults
names	group labels having the same length as l
quantiles	optional probabilities passed to quantile to show for each group
pch.quantiles	plotting character for each quantile
xlab, ylab	x- and y-axis labels
legend.text	group labels of length 2

Examples

## basic usage
pplot(split(mtcars$mpg, mtcars$vs))
pplot(mpg ~ vs, mtcars)


set.seed(1)
x <- lapply(1:5, function(x) list(rnorm(20, 0, x), rnorm(20, 0, x)))

pplot(x)
pplot(x[1], ylim = c(-3, 3))
pplot(x, test = t.test, args.test = list(paired = TRUE))
pplot(x, col = rep(2:6, each = 2), pch = c(1, 16), legend.text = c('+', '-'))
pplot(x, quantiles = 0.5, legend.text = c('+', '-'))


## pplot returns the object returned by test
pv <- pplot(
  x, quantiles = c(0.25, 0.5, 0.75), pch.quantiles = c(6, 18, 2),
  legend.text = c('+', '-'), pad = 0.1, pch = 16, bty = 'l',
  names = paste('group', 1:5), las = 1
)
sapply(pv, function(x) x$p.value)


## use a custom test function
pplot(x, test = function(x, y) cor.test(x, y, method = 'spearman'))

moods <- function(x, y) rawr::moods.test(list(x, y))
pplot(x, test = moods)
sapply(x, function(y) do.call('moods', y)$p.value)


## formula method
pplot(mpg ~ gear + am, mtcars)
pplot(mpg ~ gear + vs, mtcars, xlab = 'Gears', legend.text = c('V', 'S'))

raredd/rawr documentation built on March 4, 2024, 1:36 a.m.