Plot Log-Ratios

Displays a scatter plot.

Usage

# S4 method for class 'LogRatio,missing'
plot(
  x,
  ...,
  jitter_factor = 1,
  jitter_amount = NULL,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes
)

# S4 method for class 'GroupedLogRatio,missing'
plot(
  x,
  ...,
  jitter_factor = 1,
  jitter_amount = NULL,
  color = NULL,
  symbol = NULL,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  legend = list(x = "topright")
)

Arguments

x

A LogRatio object.

...

Further graphical parameters.

jitter_factor, jitter_amount

A length-one numeric vector specifying the amount of jitter (see jitter()).

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?

axes

A logical scalar: should axes be drawn on the plot?

frame.plot

A logical scalar: should a box be drawn around 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.

symbol

A (named) vector of colors (will be mapped to the group names of object).

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

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

See also

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

Author

N. Frerebeau

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
plot(clr)


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