1.3.trianglePlot: Triangle plots
In loa: Lattice Options and Add-Ins
1.3.trianglePlot R Documentation
Triangle plots
Description
Triangle plot functions for Lattice.
Usage
trianglePlot(x, data = NULL, ..., ref.cols = TRUE)
#standard panels
panel.trianglePlot(x = NULL, y = NULL, a0 = NULL, b0 = NULL,
c0 = NULL, ..., loa.settings = FALSE, plot = TRUE,
process = TRUE)
panel.trianglePlotFrame(..., grid = NULL, axes = NULL)
panel.trianglePlotGrid(alim = NULL, blim = NULL, clim = NULL,
..., grid = TRUE, panel.scales = NULL)
panel.trianglePlotAxes(alim = NULL, blim = NULL, clim = NULL,
..., axes = TRUE, ticks=TRUE, annotation=TRUE,
panel.scales = NULL)
#other panels
panel.triangleByGroupPolygon(x = NULL, y = NULL, a0 = NULL,
b0 = NULL, c0 = NULL, ..., loa.settings = FALSE,
plot = TRUE, process = TRUE)
panel.triangleKernelDensity(x = NULL, y = NULL, a0 = NULL,
b0 = NULL, c0 = NULL, ..., loa.settings = FALSE,
plot = TRUE, process = TRUE)
panel.triangleSurfaceSmooth(x = NULL, y = NULL, z = NULL,
a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE,
plot = TRUE, process = TRUE)
#data handlers
triABC2XY(a, b = NULL, c = NULL, ..., force.abc = TRUE,
if.na = "remove.row", if.neg = "remove.row",
verbose = FALSE)
triXY2ABC(x, y = NULL, ..., force.xy = TRUE,
verbose = FALSE)
triLimsReset(ans)
triABCSquareGrid(a, b = NULL, c = NULL, ..., n=100)
Arguments
x
For trianglePlot only, a formula in structure
z ~ a0 + b0 + c0 | cond. The elements a0, b0
and c0, the inputs for the three axis on the triangle plot,
are required, while z and conditioning (cond) are optional.
(For other functions, x may be used as the pair to y.
See y below.)
data
For trianglePlot only, if supplied, the assumed source
of the elements of formula x, typically a data.frame.
...
Additional arguments.
ref.cols
Either a logical to turn off/on grid color-coding or a
vector of colors to be applied to a0, b0 and c0 axes and grids. These are
applied to the grid lines and axes tick and annotation components. Some users,
particularly those less familiar with triangle plots, can find such color
referencing helpful when analyzing such plots. By default, the colorings are
quite subtle, so users can see the effect if them look for it but it does not
take over the plot when it is not focused on. Finer control can be achieved using
axes, ticks, grid, etc. (See below).
y, a, a0, b, b0, c, c0, z
(and x in relevant functions). a/a0 , b/b0 and
c/c0 are the three scales of the triangle plot, and x and y
are the equivalent 2-D projections. The arguments are typically options in panel functions
(panel... functions), conversion functions (triABC2XY and triXY2ABC) and
the scaling function triLimsReset. z is the z-case from the plot formula.
loa.settings, plot, process
loaPlot arguments used to manage
panelPal activity.
grid, axes, ticks, annotation
User-resets for the axes, grid, tick and annotation
elements of the plots. These can be NULL or FALSE to turn off, TRUE to show,
a vector (in which case they are assumed to be color assignments) or a list of standard plot
parameters, e.g. col, lty, lwd, etc. for color, line type and line thickness,
etc. Plot parameter assignments are applied to all axes unless specific axes are identified. For
example, trianglePlot calls including grid.col = 2 make
all axes red, while calls including grid.a0.col = 2 only
recolor the first (a0) axis.
alim, blim, clim
Delimiters for a, b and c scales, equivalent to xlim
and ylim in conventional plots, but less flexible. See Details below for
more information.
panel.scales
A local argument, typically a list, that controls the
appearance of the a0/b0/c0 axes. This is roughly equivalent to the scales
argument used by conventional lattice plots to handle x and y axis,
but intended for non-standard scales, such as the triangle axes used here.
It can be set directly or used in combination with the local scale(s) handler
function localScalesHandler to override/hijack standard scales
operations. (See note below).
force.abc, force.xy
Logicals. If a list or data.frame is supplied
to triABC2XY or triXY2ABC as a source or a/b/c or x/y respectively
should appropriately named elements be used regardless of order? See Note below.
if.na
Character. Handling method to be used if NAs are present.
The default option 'remove.row' replaces all enteries in the same row with
NAs. (Note: this is different from na.omit which would
remove the whole row. Here, the row is retained as NAs to maintain
indices for conditioning.) Other options currently include: 'make.zero'
to replace the NA with 0; and 'keep.as.is' to leave
unchanged.
if.neg
Character. Like if.na but for negative values:
'remove.row' to replace all enteries in the same row with
NAs; 'make.zero' to replace all negative values with
0; 'rescale.col' recales any column (i.e., a, b or
c) that contains a negative from zero by subtracting the minimum.
verbose
Logical, default FALSE. Should a full output be returned?
The alternative FALSE generates a minimal report.
ans
For triLimsReset only, a trellis ouput, e.g. a lattice plot,
to be scaled and plotted based on the assumption that it is a trianglePlot.
n
For triABCSquareGrid only, number of points to divide each axes by
when generating the data grid.
Details
trianglePlot generates a triangle plot using the lattice framework.
panel.trianglePlot... functions handle the appearance of triangle plot
outputs.
panel.trianglePlot, which is assigned as the default panel
manages both the data layer of the plot and the plot frame (axes, grid, annotation,
etc).
panel.trianglePlotAxes and panel.trianglePlotGrid generate
axes and grid componets of the plot, and panel.trianglePlotFrame is
a wrapper for these. The data layer, which by default is panel.loaPlot,
can be accessed separately using the data.panel argument.
triangleKernelDensity generates a kernel density surface for supplied a0,
b0 and c0 cases.
triangleSurfaceSmooth generates a smoothed surface for supplied a0,
b0, c0 and z cases.
triABC2XY converts supplied (a, b, c) coordinates to an (x, y) scale suitable
for use with triangle plot functions.
triXY2ABC converts supplied (x,y) coordinates from triangle plots to the associated
proportional (a, b, c) scale.
There are various options for range limiting with triABC2XY, triXY2ABC,
and therefore triangle plots. Firstly, limits can be set individually with
alim, blim and clim, much like with xlim and ylim for
conventional plots. However, they can also be set at once using lims, as in e.g.
lims = c(0, 1) to set all axes to full ranges, or on the basis of minimum and maximum
cut-offs using abc.mins and abc.maxs, respectively.
trianglePlot uses localScalesHandler to override normal
lattice handling of scales. This allows parameters for axes other
than 'x' and 'y' to be passed via the scales argument for
axis generation within the plot panel itself. The function does this by recovering
the information for each of the local axes (here a0, b0 and c0)
from scales, and passing this on to the plot as the argument
panel.scales which can then be evaluated by an appropriate panel...
function like panel.trianglePlotAxes. At the same time it also resets
scales to stop the standard axes being generated. The intention here is two-fold.
Firstly, to provide plot users with an axes control mechanism like the standard
scales control of x and y that they already know. And, secondly,
to provide developers with a simple framework for the quick addition of non-standard axes
or scales. See localScalesHandler and panel.localScale for
further details.
trianglePlot uses getPlotArgs to manage lattice defaults and
plot developer and user resets for the different plot components (axes, ticks, grid,
annotation). As with localScalesHandler, the intention here is to provide more
routine access to higher level plot control.
Value
trianglePlot returns trellis objects, much like
conventional lattice plot functions.
panel.trianglePlot... functions are intended for use
within a trianglePlot function call.
triABC2XY returns a list containing the named
components x and y, which are the 2-D (x,y) transformations
of supplied (a,b,c) trianglePlot elements.
triXY2ABC returns a list containing the named
components a, b and c, which are the (a,b,c)
triangle plot coordinates associated with supplied 2-D (x, y) that
trianglePlot would generate.
resetTriLims returns a supplied trellis object, rescaled
based on the assumption that it is a triangle plot.
Note
General:
With triangle plots, the (a0, b0, c0) scales are proportional. So regardless of the
absolute sizes of a coordinate set (a,b,c), values are plotted and handled
as proportions, i.e. a/(a+b+c), b/(a+b+c) and c/(a+b+c), respectively. This means
that absolute values of a, b and c are lost when points are
plotted on these axes. So, the function triXY2ABC returns the relative proportions
of a, b and c, not the absolute amounts, when translating a 2-D
(x,y) coordinates into the associated (a, b, c) coordinates.
Development:
This is an in-development plot, and 'best handling' strategies have not been decided for
several elements. So, future versions of these functions may differ significantly from the
current version.
In particular:
Current axes assignments, e.g. (a, b, c) versus (a0, b0, c0), etc., have not be finalised.
So, these may change in future versions of the function.
Currently, trianglePlot scale adjustment options have been limited. Options under
evaluation include: (1) by alim, blim, clim setting, equivalent to
xlim and ylim, (2) by lims to set all axes ranges the same, and
(3) by maxs to setting all axes range maximums and mins to set all axes
range minimums, etc.
These options are currently only avialable via the data converters.
One of the issues here is that the axes ranges are all inter-linked. The range of one axes
is a function of the other two axes ranges. So, setting these can generate contradictions.
For example, lims=c(0,0.1) should in theory set all ranges to (0, 0.1). But, the triangle
a = b = c = c(0, 0.1) cannot exist. Therefore, the plot would attempt to recover
the extended range that includes all the requested ranges (a = c(0, 0.1),
b = c(0, 0.1) and c = c(0, 0.1)), which in this case is the full
range: a = b = c = c(0, 1). Suggestions on this topic are very welcome.
trianglePlot:
As part of the loa version 0.2.19 update, trianglePlot was rewritten to run
with the most recent version of panelPal function. This means all plot
functions in loa now use the most recent version of panelPal.
This update should provide improved plot handling similar to recent versions of loaPlot
and GoogleMap functions which both already (from versions 0.2.0 onwards) use the latest
version of panelPal.
panel.trianglePlotAxes:
Code currently in revision. Please handle with care.
triABC2XY, triABCSquareGrid:
Code currently in revision. Please handle with care.
Author(s)
Karl Ropkins
References
These function makes extensive use of code developed by others.
Currently, several triangle plotting methods are under evaluation for use within
this package. These are:
The tri-plot method of Graham and Mudgley:
Graham, David J. and Mudgley, Nicholas, G. Graphical representation of particle
shape using triangular diagrams: An Excel spreadsheet method. Earth Surface
Processes and Landforms, 25, 1473-1477, 2000.
The triangle.param method of Chessel (as coded in R package 'ade4')
Dray, S. and Dufour, A.B.(2007). The ade4 package: implementing the
duality diagram for ecologists. Journal of Statistical, Software. 22(4): 1-20.
Chessel, D. and Dufour, A.B. and Thioulouse, J. (2004). The ade4 package - I -
One-table methods. R News. 4: 5-10.
Dray, S. and Dufour, A.B. and Chessel, D. (2007). The ade4 package-II: Two-table
and K-table methods. R News. 7(2): 47-52.
And the trilinear plot of Allen as reported by Zhu:
Zhu, M. (2008). How to draw a trilinear Plot. Statistical Computing & Graphics, 19(1),
June, 2008.
In this version of the package tri-plot methods are used for the triABC2XY and
triXY2ABC transforms and a modification triangle.param methods is used
to calculate suitable values for alim, blim and clim.
As elsewhere, the use of lattice is also gratefully acknowledged:
lattice:
Sarkar, Deepayan (2008). Lattice: Multivariate Data
Visualization with R. Springer, New York. ISBN
978-0-387-75968-5
See Also
In loa: For in-panel axis/scale generation, see loaPlot, panelPal,
localScalesHandler and panel.localScale.
In other packages: xyplot in lattice.
Examples
## Example 1
## Basic triangle plot usage
trianglePlot(cadmium~copper+lead+zinc|lime,
data=lat.lon.meuse)
# Notes:
# Formula structure z ~ a0 + b0 + c0 |cond, where a0, b0 and
# c0 are the three axes of the triangle plot
# Data (and groups) assignment like in standard lattice plots.
# By default z is linked to col and cex.
# Unless overridden by user inputs or group or zcase setting.
# Plot handling is similar to loaPlot
# (So, see ?loaPlot and ?panelPal for further details.)
# Formula variations:
# basic triangle plot without z values assignment
# trianglePlot(~a0+b0+c0, ...)
# ... with z values set
# trianglePlot(z~a0+b0+c0, ...)
# ... with grouping
# trianglePlot(z~a0+b0+c0, groups=grps, ...)
## Example 2
## Basic frame (axes, grid, tick, annotation) management
trianglePlot(~1+1+1, type="n",
grid.alpha = 0.2,
ticks.alpha = 0.2) ## grid and tick alpha reset
# notes:
# Here, grid and ticks arguments are used to remove or modify these
# elements of the plot frame individually.
# Setting can be management in list form like in normal lattice or
# in a loa shorthand where e.g. the argument grid.a0.lty = 1 is equivalent
# to grid = list(a0 = list(lty = 1))
# (So, quicker if you are only changing a small number of elements.)
loa documentation built on Nov. 23, 2023, 3:02 p.m.
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| 1.3.trianglePlot | R Documentation |
Triangle plots
Description
Triangle plot functions for Lattice.
Usage
trianglePlot(x, data = NULL, ..., ref.cols = TRUE)
#standard panels
panel.trianglePlot(x = NULL, y = NULL, a0 = NULL, b0 = NULL,
c0 = NULL, ..., loa.settings = FALSE, plot = TRUE,
process = TRUE)
panel.trianglePlotFrame(..., grid = NULL, axes = NULL)
panel.trianglePlotGrid(alim = NULL, blim = NULL, clim = NULL,
..., grid = TRUE, panel.scales = NULL)
panel.trianglePlotAxes(alim = NULL, blim = NULL, clim = NULL,
..., axes = TRUE, ticks=TRUE, annotation=TRUE,
panel.scales = NULL)
#other panels
panel.triangleByGroupPolygon(x = NULL, y = NULL, a0 = NULL,
b0 = NULL, c0 = NULL, ..., loa.settings = FALSE,
plot = TRUE, process = TRUE)
panel.triangleKernelDensity(x = NULL, y = NULL, a0 = NULL,
b0 = NULL, c0 = NULL, ..., loa.settings = FALSE,
plot = TRUE, process = TRUE)
panel.triangleSurfaceSmooth(x = NULL, y = NULL, z = NULL,
a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE,
plot = TRUE, process = TRUE)
#data handlers
triABC2XY(a, b = NULL, c = NULL, ..., force.abc = TRUE,
if.na = "remove.row", if.neg = "remove.row",
verbose = FALSE)
triXY2ABC(x, y = NULL, ..., force.xy = TRUE,
verbose = FALSE)
triLimsReset(ans)
triABCSquareGrid(a, b = NULL, c = NULL, ..., n=100)
Arguments
x |
For |
data |
For |
... |
Additional arguments. |
ref.cols |
Either a logical to turn off/on grid color-coding or a
vector of colors to be applied to a0, b0 and c0 axes and grids. These are
applied to the grid lines and axes tick and annotation components. Some users,
particularly those less familiar with triangle plots, can find such color
referencing helpful when analyzing such plots. By default, the colorings are
quite subtle, so users can see the effect if them look for it but it does not
take over the plot when it is not focused on. Finer control can be achieved using
|
y, a, a0, b, b0, c, c0, z |
(and |
loa.settings, plot, process |
|
grid, axes, ticks, annotation |
User-resets for the axes, grid, tick and annotation
elements of the plots. These can be |
alim, blim, clim |
Delimiters for a, b and c scales, equivalent to |
panel.scales |
A local argument, typically a list, that controls the
appearance of the a0/b0/c0 axes. This is roughly equivalent to the |
force.abc, force.xy |
Logicals. If a list or data.frame is supplied
to |
if.na |
Character. Handling method to be used if |
if.neg |
Character. Like |
verbose |
Logical, default |
ans |
For |
n |
For |
Details
trianglePlot generates a triangle plot using the lattice framework.
panel.trianglePlot... functions handle the appearance of triangle plot
outputs.
panel.trianglePlot, which is assigned as the default panel
manages both the data layer of the plot and the plot frame (axes, grid, annotation,
etc).
panel.trianglePlotAxes and panel.trianglePlotGrid generate
axes and grid componets of the plot, and panel.trianglePlotFrame is
a wrapper for these. The data layer, which by default is panel.loaPlot,
can be accessed separately using the data.panel argument.
triangleKernelDensity generates a kernel density surface for supplied a0,
b0 and c0 cases.
triangleSurfaceSmooth generates a smoothed surface for supplied a0,
b0, c0 and z cases.
triABC2XY converts supplied (a, b, c) coordinates to an (x, y) scale suitable
for use with triangle plot functions.
triXY2ABC converts supplied (x,y) coordinates from triangle plots to the associated
proportional (a, b, c) scale.
There are various options for range limiting with triABC2XY, triXY2ABC,
and therefore triangle plots. Firstly, limits can be set individually with
alim, blim and clim, much like with xlim and ylim for
conventional plots. However, they can also be set at once using lims, as in e.g.
lims = c(0, 1) to set all axes to full ranges, or on the basis of minimum and maximum
cut-offs using abc.mins and abc.maxs, respectively.
trianglePlot uses localScalesHandler to override normal
lattice handling of scales. This allows parameters for axes other
than 'x' and 'y' to be passed via the scales argument for
axis generation within the plot panel itself. The function does this by recovering
the information for each of the local axes (here a0, b0 and c0)
from scales, and passing this on to the plot as the argument
panel.scales which can then be evaluated by an appropriate panel...
function like panel.trianglePlotAxes. At the same time it also resets
scales to stop the standard axes being generated. The intention here is two-fold.
Firstly, to provide plot users with an axes control mechanism like the standard
scales control of x and y that they already know. And, secondly,
to provide developers with a simple framework for the quick addition of non-standard axes
or scales. See localScalesHandler and panel.localScale for
further details.
trianglePlot uses getPlotArgs to manage lattice defaults and
plot developer and user resets for the different plot components (axes, ticks, grid,
annotation). As with localScalesHandler, the intention here is to provide more
routine access to higher level plot control.
Value
trianglePlot returns trellis objects, much like
conventional lattice plot functions.
panel.trianglePlot... functions are intended for use
within a trianglePlot function call.
triABC2XY returns a list containing the named
components x and y, which are the 2-D (x,y) transformations
of supplied (a,b,c) trianglePlot elements.
triXY2ABC returns a list containing the named
components a, b and c, which are the (a,b,c)
triangle plot coordinates associated with supplied 2-D (x, y) that
trianglePlot would generate.
resetTriLims returns a supplied trellis object, rescaled
based on the assumption that it is a triangle plot.
Note
General:
With triangle plots, the (a0, b0, c0) scales are proportional. So regardless of the
absolute sizes of a coordinate set (a,b,c), values are plotted and handled
as proportions, i.e. a/(a+b+c), b/(a+b+c) and c/(a+b+c), respectively. This means
that absolute values of a, b and c are lost when points are
plotted on these axes. So, the function triXY2ABC returns the relative proportions
of a, b and c, not the absolute amounts, when translating a 2-D
(x,y) coordinates into the associated (a, b, c) coordinates.
Development:
This is an in-development plot, and 'best handling' strategies have not been decided for several elements. So, future versions of these functions may differ significantly from the current version.
In particular:
Current axes assignments, e.g. (a, b, c) versus (a0, b0, c0), etc., have not be finalised. So, these may change in future versions of the function.
Currently, trianglePlot scale adjustment options have been limited. Options under
evaluation include: (1) by alim, blim, clim setting, equivalent to
xlim and ylim, (2) by lims to set all axes ranges the same, and
(3) by maxs to setting all axes range maximums and mins to set all axes
range minimums, etc.
These options are currently only avialable via the data converters.
One of the issues here is that the axes ranges are all inter-linked. The range of one axes
is a function of the other two axes ranges. So, setting these can generate contradictions.
For example, lims=c(0,0.1) should in theory set all ranges to (0, 0.1). But, the triangle
a = b = c = c(0, 0.1) cannot exist. Therefore, the plot would attempt to recover
the extended range that includes all the requested ranges (a = c(0, 0.1),
b = c(0, 0.1) and c = c(0, 0.1)), which in this case is the full
range: a = b = c = c(0, 1). Suggestions on this topic are very welcome.
trianglePlot:
As part of the loa version 0.2.19 update, trianglePlot was rewritten to run
with the most recent version of panelPal function. This means all plot
functions in loa now use the most recent version of panelPal.
This update should provide improved plot handling similar to recent versions of loaPlot
and GoogleMap functions which both already (from versions 0.2.0 onwards) use the latest
version of panelPal.
panel.trianglePlotAxes:
Code currently in revision. Please handle with care.
triABC2XY, triABCSquareGrid:
Code currently in revision. Please handle with care.
Author(s)
Karl Ropkins
References
These function makes extensive use of code developed by others.
Currently, several triangle plotting methods are under evaluation for use within this package. These are:
The tri-plot method of Graham and Mudgley:
Graham, David J. and Mudgley, Nicholas, G. Graphical representation of particle shape using triangular diagrams: An Excel spreadsheet method. Earth Surface Processes and Landforms, 25, 1473-1477, 2000.
The triangle.param method of Chessel (as coded in R package 'ade4')
Dray, S. and Dufour, A.B.(2007). The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical, Software. 22(4): 1-20.
Chessel, D. and Dufour, A.B. and Thioulouse, J. (2004). The ade4 package - I - One-table methods. R News. 4: 5-10.
Dray, S. and Dufour, A.B. and Chessel, D. (2007). The ade4 package-II: Two-table and K-table methods. R News. 7(2): 47-52.
And the trilinear plot of Allen as reported by Zhu:
Zhu, M. (2008). How to draw a trilinear Plot. Statistical Computing & Graphics, 19(1), June, 2008.
In this version of the package tri-plot methods are used for the triABC2XY and
triXY2ABC transforms and a modification triangle.param methods is used
to calculate suitable values for alim, blim and clim.
As elsewhere, the use of lattice is also gratefully acknowledged:
lattice: Sarkar, Deepayan (2008). Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
See Also
In loa: For in-panel axis/scale generation, see loaPlot, panelPal,
localScalesHandler and panel.localScale.
In other packages: xyplot in lattice.
Examples
## Example 1
## Basic triangle plot usage
trianglePlot(cadmium~copper+lead+zinc|lime,
data=lat.lon.meuse)
# Notes:
# Formula structure z ~ a0 + b0 + c0 |cond, where a0, b0 and
# c0 are the three axes of the triangle plot
# Data (and groups) assignment like in standard lattice plots.
# By default z is linked to col and cex.
# Unless overridden by user inputs or group or zcase setting.
# Plot handling is similar to loaPlot
# (So, see ?loaPlot and ?panelPal for further details.)
# Formula variations:
# basic triangle plot without z values assignment
# trianglePlot(~a0+b0+c0, ...)
# ... with z values set
# trianglePlot(z~a0+b0+c0, ...)
# ... with grouping
# trianglePlot(z~a0+b0+c0, groups=grps, ...)
## Example 2
## Basic frame (axes, grid, tick, annotation) management
trianglePlot(~1+1+1, type="n",
grid.alpha = 0.2,
ticks.alpha = 0.2) ## grid and tick alpha reset
# notes:
# Here, grid and ticks arguments are used to remove or modify these
# elements of the plot frame individually.
# Setting can be management in list form like in normal lattice or
# in a loa shorthand where e.g. the argument grid.a0.lty = 1 is equivalent
# to grid = list(a0 = list(lty = 1))
# (So, quicker if you are only changing a small number of elements.)
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