Package 'isopleuros'

Arctic Lake Sediments Compositions

Description

Sand, silt, clay compositions of 39 sediment samples at different water depths in an Arctic lake.

Usage

arctic

Format

A data.frame with 4 variables:

sand

silt

clay

depth

Water depth (m).

Source

Aitchison, J. (1986). The Statistical Analysis of Compositional Data. London: Chapman and Hall. doi:10.1007/978-94-009-4109-0.

See Also

Other datasets: boxite, lava

---

Boxite Compositions

Description

Compositions of 25 specimens of boxite.

Usage

boxite

Format

A data.frame with 5 variables:

A

albite.

B

blandite.

C

cornite.

D

daubite.

E

endite.

Source

Aitchison, J. (1986). The Statistical Analysis of Compositional Data. London: Chapman and Hall. doi:10.1007/978-94-009-4109-0.

See Also

Other datasets: arctic, lava

---

Skye Lavas Compositions

Description

AFM compositions of 23 aphyric Skye lavas.

Usage

lava

Format

A data.frame with 3 variables:

A

Na2O + K2O (percent).

F

Fe2O3 (percent).

M

MgO (percent).

Source

Aitchison, J. (1986). The Statistical Analysis of Compositional Data. London: Chapman and Hall. doi:10.1007/978-94-009-4109-0.

See Also

Other datasets: arctic, boxite

---

Add Arrows to a Ternary Plot

Description

Draw arrows between pairs of points.

Usage

ternary_arrows(x0, y0, z0, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_arrows(x0, y0, z0, x1 = x0, y1 = y0, z1 = z0, ...)

Arguments

x0, y0, z0	A numeric vector giving the x, y and z ternary coordinates of points from which to draw.
...	Further arguments to be passed to graphics::arrows().
x1, y1, z1	A numeric vector giving the x, y and z ternary coordinates of points to which to draw.

Value

ternary_arrows() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::arrows()

Other geometries: ternary_crosshairs(), ternary_labels(), ternary_lines(), ternary_points(), ternary_polygon(), ternary_segments(), ternary_text()

Examples

## Add arrows
ternary_plot(NULL, panel.first = ternary_grid())
ternary_arrows(x0 = 40, y0 = 20, z0 = 40,
               x1 = 20, y1 = 40, z1 = 40)

---

Add an Axis to a Ternary Plot

Description

Adds an axis to the current plot.

Usage

ternary_axis(
  side,
  at = NULL,
  labels = TRUE,
  tick = TRUE,
  center = getOption("isopleuros.center"),
  scale = getOption("isopleuros.scale"),
  font = NA,
  lty = "solid",
  lwd = 1,
  lwd.ticks = lwd,
  col = NULL,
  col.ticks = NULL,
  ...
)

Arguments

side	An integer specifying which side of the plot the axis is to be drawn on. The axis is placed as follows: 1=below, 2=right and 3=left.
at	A numeric vector giving the points at which tick-marks are to be drawn.
labels	A logical scalar specifying whether (numerical) annotations are to be made at the tickmarks, or a character vector of labels to be placed at the tickpoints. If this is not logical, at should also be supplied and of the same length.
tick	A logical scalar: should tickmarks and an axis line be drawn?
center	A numeric vector giving the center. If NULL (the default), data are assumed not centered.
scale	A numeric vector giving the scale factor. If NULL (the default), data are assumed not scaled.
font	font for text. Defaults to par("font.axis").
lty	A character string or numeric value specifying the line type for both the axis line and the tick marks.
lwd, lwd.ticks	A non-negative numeric value specifying the line widths for the axis line and the tick marks.
col, col.ticks	Colors for the axis line and the tick marks respectively. Defaults to par("col.axis").
...	Other graphical parameters may also be passed as arguments to this function, particularly, cex.axis, col.axis and font.axis for axis annotation.

Value

ternary_axis() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other graphical elements: ternary_box(), ternary_grid(), ternary_pairs(), ternary_plot(), ternary_title()

Examples

## Add axis
ternary_plot(NULL, axes = FALSE)
ternary_axis(side = 1, col = "red")
ternary_axis(side = 2, col = "blue")
ternary_axis(side = 3, col = "green")

## Add box and grid
ternary_plot(NULL, axes = FALSE)
ternary_box(lty = "dashed", col = "red")
ternary_grid(lty.primary = "dotted")

---

Draw a Box around a Ternary Plot

Description

Draw a Box around a Ternary Plot

Usage

ternary_box(lty = "solid", ...)

Arguments

lty	A character string or numeric value specifying the line type of the box.
...	Other graphical parameters may also be passed as arguments to this function, particularly, col or lwd.

Value

ternary_box() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other graphical elements: ternary_axis(), ternary_grid(), ternary_pairs(), ternary_plot(), ternary_title()

Examples

## Add axis
ternary_plot(NULL, axes = FALSE)
ternary_axis(side = 1, col = "red")
ternary_axis(side = 2, col = "blue")
ternary_axis(side = 3, col = "green")

## Add box and grid
ternary_plot(NULL, axes = FALSE)
ternary_box(lty = "dashed", col = "red")
ternary_grid(lty.primary = "dotted")

---

Contour Lines

Description

Computes and draws contour lines.

Usage

ternary_contour(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_contour(
  x,
  y,
  z,
  value,
  n = 50,
  nlevels = 10,
  levels = pretty(range(value, na.rm = TRUE), nlevels),
  ilr = TRUE,
  method = "linear",
  extrapolate = FALSE,
  palette = function(i) grDevices::hcl.colors(i, "YlOrRd", rev = TRUE),
  ...
)

## S4 method for signature 'ANY,missing,missing'
ternary_contour(
  x,
  value,
  n = 50,
  nlevels = 10,
  levels = pretty(range(value, na.rm = TRUE), nlevels),
  ilr = TRUE,
  method = "linear",
  extrapolate = FALSE,
  palette = function(i) grDevices::hcl.colors(i, "YlOrRd", rev = TRUE),
  ...
)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to ternary_lines().
value	A numeric vector giving the values to be plotted.
n	A length-one numeric specifying the number of grid points.
nlevels	A length-one numeric vector specifying the number of contour levels desired. Only used if levels is NULL.
levels	A numeric vector of levels at which to draw contour lines.
ilr	A logical scalar: should interpolation be computed in ILR space? If FALSE, interpolation is computed in Cartesian space.
method	A character string: specifying the method for interpolation (see interp::interp()).
extrapolate	A logical scalar: should extrapolation be used outside of the convex hull determined by the data points (see interp::interp())?
palette	A color palette function that takes a single integer argument (the number of levels) and returns a vector of colors.

Details

Contour are computed from a bivariate interpolation onto a grid, after an isometric log ratio transformation of the original data.

Value

ternary_contour() is called it for its side-effects.

Invisibly returns a list with elements levels (the contour levels) and colors (the contour colors) that can be used for a legend.

Note

The interp package needs to be installed on your machine.

Author(s)

N. Frerebeau

See Also

interp::interp(), grDevices::contourLines()

Other statistics: ternary_density(), ternary_ellipse(), ternary_hull(), ternary_mean(), ternary_pca()

Examples

## Add density
## Data from Aitchison 1986
ternary_plot(arctic, panel.first = ternary_grid())
levels <- ternary_contour(arctic, value = arctic$depth, n = 100, nlevels = 10)

## Add a legend
legend_image <- grDevices::as.raster(rev(levels$colors))
graphics::rasterImage(legend_image, 0.85, 0.75, 0.9, 1)
graphics::text(x = 0.9, y = c(0.75, 1), labels = range(levels$levels), pos = 4)

---

Add Cross-Hairs to a Ternary Plot

Description

Draw lines that intersect at a point.

Usage

ternary_crosshairs(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_crosshairs(x, y, z, x_mark = TRUE, y_mark = TRUE, z_mark = TRUE, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_crosshairs(x, x_mark = TRUE, y_mark = TRUE, z_mark = TRUE, ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further graphical parameters (see graphics::par()) may also be supplied as arguments, particularly, line type, lty, line width, lwd and color, col. Also the line characteristics lend, ljoin and lmitre.
x_mark, y_mark, z_mark	A logical scalar: should the x, y or z axis component be drawn?

Value

ternary_crosshairs() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other geometries: ternary_arrows(), ternary_labels(), ternary_lines(), ternary_points(), ternary_polygon(), ternary_segments(), ternary_text()

Examples

## Add cross-hairs
## Data from Aitchison 1986
ternary_plot(lava, panel.first = ternary_grid())
ternary_crosshairs(lava)

ternary_plot(lava, panel.first = ternary_grid())
ternary_crosshairs(lava, y_mark = FALSE, z_mark = FALSE, col = "red")

ternary_plot(lava, panel.first = ternary_grid())
ternary_crosshairs(lava, x_mark = FALSE, z_mark = FALSE, col = "green")

ternary_plot(lava, panel.first = ternary_grid())
ternary_crosshairs(lava, x_mark = FALSE, y_mark = FALSE, col = "blue")

---

Density Contour Lines

Description

Computes and draws density contour lines.

Usage

ternary_density(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_density(
  x,
  y,
  z,
  h = NULL,
  n = 25,
  nlevels = 10,
  levels = NULL,
  palette = function(i) grDevices::hcl.colors(i, "YlOrRd", rev = TRUE),
  ...
)

## S4 method for signature 'ANY,missing,missing'
ternary_density(
  x,
  h = NULL,
  n = 25,
  nlevels = 10,
  levels = NULL,
  palette = function(i) grDevices::hcl.colors(i, "YlOrRd", rev = TRUE),
  ...
)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to ternary_lines().
h	A length-one numeric vector giving the bandwidth.
n	A length-one numeric specifying the number of grid points.
nlevels	A length-one numeric vector specifying the number of contour levels desired. Only used if levels is NULL.
levels	A numeric vector of levels at which to draw contour lines.
palette	A color palette function that takes a single integer argument (the number of levels) and returns a vector of colors.

Details

Two-dimensional kernel density estimation with an axis-aligned bivariate normal kernel. Normal kernel is evaluated on a square grid, after an isometric log ratio transformation of the original data.

Value

ternary_density() is called it for its side-effects.

Invisibly returns a list with elements levels (the contour levels) and colors (the contour colors) that can be used for a legend.

Note

Two-dimensional kernel density estimation is adapted from MASS::kde2d().

This must be considered as experimental and subject to major changes in a future release.

Author(s)

N. Frerebeau

See Also

grDevices::contourLines()

Other statistics: ternary_contour(), ternary_ellipse(), ternary_hull(), ternary_mean(), ternary_pca()

Examples

## Add density
## Data from Aitchison 1986
ternary_plot(lava, panel.first = ternary_grid())
levels <- ternary_density(lava, n = 500, nlevels = 10)

## Add a legend
legend_image <- grDevices::as.raster(rev(levels$colors))
graphics::rasterImage(legend_image, 0.85, 0.75, 0.9, 1)
graphics::text(x = 0.9, y = c(0.75, 1), labels = range(levels$levels), pos = 4)

---

Add an Ellipse to a Ternary Plot

Description

Computes and draws a confidence/tolerance ellipse.

Usage

ternary_ellipse(x, y, z, ...)

ternary_confidence(x, y, z, ...)

ternary_tolerance(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_ellipse(x, y, z, radius = 1, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_ellipse(x, radius = 1, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_confidence(x, y, z, level = 0.95, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_confidence(x, level = 0.95, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_tolerance(x, y, z, level = 0.95, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_tolerance(x, level = 0.95, ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to graphics::polygon().
radius	A numeric vector specifying the scaling of the half-diameters.
level	A numeric vector specifying the confidence/tolerance level.

Details

Ellipse coordinates are computed after an isometric log ratio transformation of the original data.

Value

ternary_ellipse() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::polygon()

Other statistics: ternary_contour(), ternary_density(), ternary_hull(), ternary_mean(), ternary_pca()

Examples

## Ellipses
## Data from Aitchison 1986
ternary_plot(lava, panel.first = ternary_grid(5, 10))
ternary_tolerance(lava, level = 0.95, border = "blue", lty = 2)
ternary_confidence(lava, level = 0.95, border = "red", lty = 3)

---

Add Grid to a Ternary Plot

Description

Adds a triangular grid to an existing plot.

Usage

ternary_grid(
  primary = NULL,
  secondary = NULL,
  center = getOption("isopleuros.center"),
  scale = getOption("isopleuros.scale"),
  col.primary = "darkgray",
  col.secondary = "lightgray",
  lty.primary = "dashed",
  lty.secondary = "dotted",
  lwd.primary = 1,
  lwd.secondary = lwd.primary
)

Arguments

primary	An integer specifying the number of cells of the primary grid in x, y and z direction.
secondary	An integer specifying the number of cells of the secondary grid in x, y and z direction.
center	A numeric vector giving the center. If NULL (the default), data are assumed not centered.
scale	A numeric vector giving the scale factor. If NULL (the default), data are assumed not scaled.
col.primary, col.secondary	A character string specifying the color of the grid lines.
lty.primary, lty.secondary	A character string or numeric value specifying the line type of the grid lines.
lwd.primary, lwd.secondary	A non-negative numeric value specifying the line width of the grid lines.

Value

ternary_grid() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other graphical elements: ternary_axis(), ternary_box(), ternary_pairs(), ternary_plot(), ternary_title()

Examples

## Data from Aitchison 1986
ternary_plot(lava, center = FALSE, scale = FALSE, col = "red", pch = 16)
ternary_grid(5)

## Center
z <- ternary_plot(lava, center = TRUE, col = "blue", pch = 16)
ternary_grid(5, center = z$center)

## Center and scale
z <- ternary_plot(lava, center = TRUE, scale = TRUE, col = "green", pch = 16)
ternary_grid(5, center = z$center, scale = z$scale)

---

Convex Hull of a Set of Points

Description

Computes and draws the convex hull of the set of points specified.

Usage

ternary_hull(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_hull(x, y, z, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_hull(x, y, z, ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to graphics::polygon().

Value

ternary_hull() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

grDevices::chull(), graphics::polygon()

Other statistics: ternary_contour(), ternary_density(), ternary_ellipse(), ternary_mean(), ternary_pca()

Examples

## Convex hull
## Data from Aitchison 1986
ternary_plot(lava, panel.first = ternary_grid(5, 10))
ternary_hull(lava, border = "red")

---

Non-Overlapping Text Labels

Description

Optimize the location of text labels to minimize overplotting text.

Usage

ternary_labels(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_labels(x, y, z, labels = seq_along(x), ...)

## S4 method for signature 'ANY,missing,missing'
ternary_labels(x, labels = seq_along(x$x), ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further graphical parameters (see graphics::par()) may also be supplied as arguments, particularly, character expansion, cex and color, col.
labels	A character vector or expression specifying the text to be written.

Value

ternary_labels() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::text()

Other geometries: ternary_arrows(), ternary_crosshairs(), ternary_lines(), ternary_points(), ternary_polygon(), ternary_segments(), ternary_text()

Examples

## Compositional data
coda <- data.frame(
  X = c(41.0, 40, 39.0),
  Y = c(19.5, 20, 20.5),
  Z = c(39.5, 40, 40.5)
)

## Add text
ternary_plot(NULL, panel.first = ternary_grid())
ternary_points(coda)
ternary_labels(coda, labels = c("A", "B", "C"))

---

Add Connected Line Segments to a Ternary Plot

Description

Add Connected Line Segments to a Ternary Plot

Usage

ternary_lines(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_lines(x, y, z, type = "l", ...)

## S4 method for signature 'ANY,missing,missing'
ternary_lines(x, type = "l", ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further graphical parameters (see graphics::par()) may also be supplied as arguments, particularly, line type, lty, line width, lwd, color, col and for type = "b", pch. Also the line characteristics lend, ljoin and lmitre.
type	A character string indicating the type of plotting; actually any of the types as in graphics::plot.default().

Value

ternary_lines() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::lines()

Other geometries: ternary_arrows(), ternary_crosshairs(), ternary_labels(), ternary_points(), ternary_polygon(), ternary_segments(), ternary_text()

Examples

## Compositional data
coda <- data.frame(
  X = c(20, 60, 20, 20),
  Y = c(20, 20, 60, 40),
  Z = c(60, 20, 20, 40)
)

## Add lines
ternary_plot(NULL, panel.first = ternary_grid())
ternary_lines(coda, col = "red", lwd = 2)

---

Compositional Mean

Description

Computes and draws the closed geometric mean of the set of points specified.

Usage

ternary_mean(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_mean(x, y, z, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_mean(x, y, z, ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to graphics::points().

Value

ternary_mean() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other statistics: ternary_contour(), ternary_density(), ternary_ellipse(), ternary_hull(), ternary_pca()

Examples

## Mean
## Data from Aitchison 1986
ternary_plot(lava, panel.first = ternary_grid())
ternary_mean(lava, pch = 16, col = "red")
ternary_confidence(lava, level = 0.95, border = "red", lty = 1)

---

Ternary Plot Matrices

Description

Produces a matrix of ternary plots.

Usage

ternary_pairs(x, ...)

## S4 method for signature 'matrix'
ternary_pairs(x, margin = NULL, ...)

## S4 method for signature 'data.frame'
ternary_pairs(x, margin = NULL, ...)

Arguments

x	A matrix or a data.frame. Columns are converted to numeric in the same way that data.matrix() does.
...	Further graphical parameters.
margin	A character string or an integer giving the index of the column to be used as the third part of the ternary plots. If NULL (the default), marginal compositions will be used (i.e. the geometric mean of the non-selected parts).

Value

ternary_pairs() is called it for its side-effects: it results in a graphic being displayed. Invisibly returns x.

Author(s)

N. Frerebeau

See Also

Other graphical elements: ternary_axis(), ternary_box(), ternary_grid(), ternary_plot(), ternary_title()

Examples

## Data from Aitchison 1986
## Ternary plots with marginal compositions
ternary_pairs(boxite)

## Ternary plots with endite
ternary_pairs(boxite, margin = "E")

---

Principal Component Analysis

Description

Computes and draws principal component.

Usage

ternary_pca(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_pca(x, y, z, axis = 1, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_pca(x, axis = 1, ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to graphics::lines().
axis	An integer specifying the dimension to be plotted.

Value

ternary_pca() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other statistics: ternary_contour(), ternary_density(), ternary_ellipse(), ternary_hull(), ternary_mean()

Examples

## PCA
## Data from Aitchison 1986
ternary_plot(lava, panel.first = ternary_grid())
ternary_pca(lava, axis = 1, col = "red", lty = 2)

---

Ternary Plot

Description

Produces a ternary plot.

Usage

ternary_plot(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_plot(
  x,
  y,
  z,
  center = FALSE,
  scale = FALSE,
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  xlab = NULL,
  ylab = NULL,
  zlab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  ...
)

## S4 method for signature 'ANY,missing,missing'
ternary_plot(
  x,
  xlim = NULL,
  ylim = NULL,
  zlim = NULL,
  xlab = NULL,
  ylab = NULL,
  zlab = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  ...
)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Other graphical parameters may also be passed as arguments to this function.
center	A logical scalar: should the data be centered?
scale	A logical scalar: should the data be scaled?
xlim	A length-two numeric vector giving the x limits in the range $[0,1]$.
ylim	A length-two numeric vector giving the y limits in the range $[0,1]$.
zlim	A length-two numeric vector giving the z limits in the range $[0,1]$.
xlab, ylab, zlab	A character string giving a label for the x, y and z axes.
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, y and z 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?
panel.first	An an expression to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.
panel.last	An expression to be evaluated after plotting has taken place but before the axes, title and box are added.

Value

ternary_plot() is called it for its side-effects: it results in a graphic being displayed. Invisibly returns a list with the components:

x	A numeric vector of x values.
y	A numeric vector of y values.
z	A numeric vector of z values.
center	A numeric vector giving the center.
scale	A numeric vector giving the scale factor.

Author(s)

N. Frerebeau

See Also

Other graphical elements: ternary_axis(), ternary_box(), ternary_grid(), ternary_pairs(), ternary_title()

Examples

## Blank plot
ternary_plot(NULL)

## Compositional data
coda <- data.frame(
  X = c(20, 60, 20, 1/3),
  Y = c(20, 20, 60, 1/3),
  Z = c(60, 20, 20, 1/3)
)

## Ternary plot
ternary_plot(coda, pch = 16, col = "red")

## Add a grid
ternary_plot(coda, panel.first = ternary_grid(5, 10))

## Zoom
ternary_plot(coda, xlim = c(0.5, 1), panel.first = ternary_grid())
ternary_plot(coda, ylim = c(0.5, 1), panel.first = ternary_grid())
ternary_plot(coda, zlim = c(0.5, 1), panel.first = ternary_grid())

## Color according to a supplementary variable
## Data from Aitchison 1986
col <- grDevices::colorRampPalette(c("red", "blue"))(nrow(arctic))
ternary_plot(arctic, panel.first = ternary_grid(), pch = 16, col = col)

---

Add Points to a Ternary Plot

Description

Add Points to a Ternary Plot

Usage

ternary_points(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_points(x, y, z, center = FALSE, scale = FALSE, type = "p", ...)

## S4 method for signature 'ANY,missing,missing'
ternary_points(x, center = FALSE, scale = FALSE, type = "p", ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further graphical parameters (see graphics::par()) may also be supplied as arguments, particularly, plotting character, pch, character expansion, cex and color, col.
center	A logical scalar: should the data be centered?
scale	A logical scalar: should the data be scaled?
type	A character string indicating the type of plotting; actually any of the types as in graphics::plot.default().

Value

ternary_points() is called it for its side-effects. Invisibly returns a list with the components:

x	A numeric vector of x values.
y	A numeric vector of y values.
z	A numeric vector of z values.
center	A numeric vector giving the center.
scale	A numeric vector giving the scale factor.

Author(s)

N. Frerebeau

See Also

graphics::points()

Other geometries: ternary_arrows(), ternary_crosshairs(), ternary_labels(), ternary_lines(), ternary_polygon(), ternary_segments(), ternary_text()

Examples

## Add points
## Data from Aitchison 1986
ternary_plot(NULL, panel.first = ternary_grid())
ternary_points(lava, col = "red", pch = 16)

## Center and scale
ternary_plot(NULL, axes = FALSE, frame.plot = TRUE)
ternary_points(lava, col = "red", pch = 16)
ternary_points(lava, center = TRUE, col = "blue", pch = 16)
ternary_points(lava, center = TRUE, scale = TRUE, col = "green", pch = 16)

---

Polygon Drawing

Description

Draws the polygons whose vertices are given in x, y and z.

Usage

ternary_polygon(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_polygon(x, y, z, ...)

## S4 method for signature 'ANY,missing,missing'
ternary_polygon(x, y, z, ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to graphics::polygon().

Value

ternary_polygon() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::polygon()

Other geometries: ternary_arrows(), ternary_crosshairs(), ternary_labels(), ternary_lines(), ternary_points(), ternary_segments(), ternary_text()

Examples

## Compositional data
coda <- data.frame(
  X = c(20, 60, 20),
  Y = c(20, 20, 60),
  Z = c(60, 20, 20)
)

## Add a polygon
ternary_plot(NULL, panel.first = ternary_grid())
ternary_polygon(coda, density = 5, border = "red")

---

Add Line Segments to a Ternary Plot

Description

Draw line segments between pairs of points.

Usage

ternary_segments(x0, y0, z0, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_segments(x0, y0, z0, x1 = x0, y1 = y0, z1 = z0, ...)

Arguments

x0, y0, z0	A numeric vector giving the x, y and z ternary coordinates of points from which to draw.
...	Further graphical parameters (see graphics::par()) may also be supplied as arguments, particularly, line type, lty, line width, lwd and color, col. Also the line characteristics lend, ljoin and lmitre.
x1, y1, z1	A numeric vector giving the x, y and z ternary coordinates of points to which to draw.

Value

ternary_segments() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::segments()

Other geometries: ternary_arrows(), ternary_crosshairs(), ternary_labels(), ternary_lines(), ternary_points(), ternary_polygon(), ternary_text()

Examples

## Add segments
ternary_plot(NULL, panel.first = ternary_grid())
ternary_segments(x0 = 40, y0 = 20, z0 = 40,
                 x1 = 20, y1 = 40, z1 = 40)

---

Add Text to a Ternary Plot

Description

Draws the strings given in the vector labels at the coordinates given by x, y and z.

Usage

ternary_text(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
ternary_text(x, y, z, labels = seq_along(x), ...)

## S4 method for signature 'ANY,missing,missing'
ternary_text(x, labels = seq_along(x$x), ...)

Arguments

x, y, z	A numeric vector giving the x, y and z ternary coordinates of a set of points. If y and z are missing, an attempt is made to interpret x in a suitable way (see grDevices::xyz.coords()).
...	Further arguments to be passed to graphics::text().
labels	A character vector or expression specifying the text to be written.

Value

ternary_text() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

graphics::text()

Other geometries: ternary_arrows(), ternary_crosshairs(), ternary_labels(), ternary_lines(), ternary_points(), ternary_polygon(), ternary_segments()

Examples

## Compositional data
coda <- data.frame(
  X = c(20, 60, 20),
  Y = c(20, 20, 60),
  Z = c(60, 20, 20)
)

## Add text
ternary_plot(NULL, panel.first = ternary_grid())
ternary_text(coda, labels = c("A", "B", "C"), col = "red", cex = 2)

---

Ternary Plot Annotation

Description

Ternary Plot Annotation

Usage

ternary_title(
  main = NULL,
  sub = NULL,
  xlab = NULL,
  ylab = NULL,
  zlab = NULL,
  line = NA,
  outer = FALSE,
  ...
)

Arguments

main	A character string specifying the main title (on top).
sub	A character string specifying the sub-title (at bottom).
xlab, ylab, zlab	A character string giving a label for the x, y and z axes.
line	Specifying a value for line overrides the default placement of labels, and places them this many lines outwards from the plot edge.
outer	A logical scalar: should the titles be placed in the outer margins of the plot?
...	Other graphical parameters may also be passed as arguments to this function, particularly, font.main, cex.main, col.main and font.sub, cex.sub, col.sub for title annotation; font.lab, cex.lab and col.lab for axis label.

Value

ternary_title() is called it for its side-effects.

Author(s)

N. Frerebeau

See Also

Other graphical elements: ternary_axis(), ternary_box(), ternary_grid(), ternary_pairs(), ternary_plot()

Examples

## Add title
ternary_plot(NULL, main = "Main title", sub = "Subtitle",
             xlab = "A", ylab = "B", zlab = "C")

ternary_plot(NULL, ann = FALSE)
ternary_title(main = "Main title", sub = "Subtitle",
              xlab = "A", ylab = "B", zlab = "C")

---

Ceramic Phase Diagram

Description

Ceramic Phase Diagram

Usage

triangle_phase_cas(labels = TRUE, symbol = FALSE, mol = FALSE, ...)

triangle_phase_ceramic(labels = TRUE, symbol = FALSE, mol = FALSE, ...)

Arguments

labels	A logical scalar: should labels be displayed?
symbol	A logical scalar: should symbol be used instead of full labels? Only used if labels is TRUE.
mol	A logical scalar: should molarity be used instead of molar mass?
...	Further arguments to be passed to graphics::polygon().

Author(s)

N. Frerebeau

See Also

Other charts: triangle_soil

Examples

## Ceramic phase diagram
ternary_plot(NULL, xlab = "CaO", ylab = "Al2O3", zlab = "SiO2")
triangle_phase_ceramic(symbol = TRUE, mol = TRUE, pch = 16)

ternary_plot(NULL, xlab = "CaO", ylab = "Al2O3", zlab = "SiO2")
triangle_phase_ceramic(symbol = TRUE, mol = FALSE, pch = 16)

## CAS diagram
ternary_plot(NULL, axes = FALSE, ann = FALSE, frame.plot = TRUE)
triangle_phase_cas(mol = FALSE, pch = 16)

---

Soil Texture Triangle

Description

Soil Texture Triangle

Usage

triangle_soil_hypres(labels = TRUE, symbol = FALSE, ...)

triangle_soil_folk(labels = TRUE, symbol = FALSE, ...)

triangle_soil_shepard(labels = TRUE, symbol = FALSE, ...)

triangle_soil_usda(labels = TRUE, symbol = FALSE, ...)

Arguments

labels	A logical scalar: should labels be displayed?
symbol	A logical scalar: should symbol be used instead of full labels? Only used if labels is TRUE.
...	Further arguments to be passed to graphics::polygon().

Author(s)

N. Frerebeau

See Also

Other charts: triangle_phase_cas()

Examples

## HYPRES soil texture
ternary_plot(NULL, xlab = "sand", ylab = "silt", zlab = "clay")
triangle_soil_hypres()

## USDA (1951) soil texture
ternary_plot(NULL, xlab = "sand", ylab = "silt", zlab = "clay")
triangle_soil_usda(symbol = TRUE)

## Folk (1954) soil texture
ternary_plot(NULL, xlab = "sand", ylab = "silt", zlab = "clay")
triangle_soil_folk(symbol = TRUE)

## Shepard (1954) soil texture
ternary_plot(NULL, xlab = "sand", ylab = "silt", zlab = "clay")
triangle_soil_shepard()

---