nexus (version 0.6.0)

boxplot: Boxplot of Log-Ratios

Description

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

Usage

# S4 method for 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 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")
)

Value

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

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.

Author

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)