boxplot: Boxplot of Log-Ratios

In nexus: Sourcing Archaeological Materials by Chemical Composition

Boxplot of Log-Ratios

Description

Displays box-and-whisker plots of the given (grouped) values.

Usage

## S4 method for signature 'LogRatio'
boxplot(
  x,
  ...,
  range = 1.5,
  width = NULL,
  varwidth = FALSE,
  notch = FALSE,
  outline = TRUE,
  plot = TRUE,
  horizontal = FALSE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann")
)

## S4 method for signature 'GroupedLogRatio'
boxplot(
  x,
  ...,
  range = 1.5,
  width = NULL,
  varwidth = FALSE,
  notch = FALSE,
  outline = TRUE,
  plot = TRUE,
  horizontal = FALSE,
  color = NULL,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  legend = list(x = "topright")
)

Arguments

x	A LogRatio object.
...	Further graphical parameters.
range	A length-one numeric vector specifying how far the plot whiskers extend out from the box (see graphics::boxplot()).
width	A numeric vector giving the relative widths of the boxes making up the plot.
varwidth	A logical scalar: should the boxes be drawn with widths proportional to the square-roots of the number of observations in the groups?
notch	A logical scalar: should a notch be drawn in each side of the boxes?
outline	A logical scalar: should the outliers be drawn?
plot	A logical scalar: should a boxplot be produced? If FALSE, the summaries which the boxplots are based on are invisibly returned.
horizontal	A logical scalar: should the boxplots be horizontal?
xlab, ylab	A character vector giving the x and y axis labels.
main	A character string giving a main title for the plot.
sub	A character string giving a subtitle for the plot.
ann	A logical scalar: should the default annotation (title and x and y axis labels) appear on the plot?
color	A (named) vector of colors (will be mapped to the group names of object) or a function that when called with a single argument (an integer specifying the number of colors) returns a vector of colors.
legend	A list of additional arguments to be passed to graphics::legend(); names of the list are used as argument names. If NULL, no legend is displayed.

Value

boxplot() is called for its side-effects: is results in a graphic being displayed (invisibly return x).

Author(s)

N. Frerebeau

See Also

graphics::boxplot()

Other plot methods: as_graph(), barplot(), hist(), pairs(), plot()

Examples

## Data from Day et al. 2011
data("kommos", package = "folio")
kommos <- remove_NA(kommos, margin = 1) # Remove cases with missing values
coda <- as_composition(kommos, parts = 3:22) # Coerce to compositional data

## Log ratio
clr <- transform_clr(coda)

## Boxplot
boxplot(clr)

## Use ceramic types for grouping
grp <- group(coda, by = kommos$type)
clr <- transform_clr(grp)
boxplot(clr)

nexus documentation built on June 8, 2025, 11:12 a.m.