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 compositions: Compositional Data Analysis
 plot3dacomp: 3Dplot of compositional data
3Dplot of compositional data
Description
3Dplot of compositional data. The plot is mainly an exploratory tool, not intended for exact display of data.
Usage
1 2 3 4 5 6 7 8 9 10  ## S3 method for class 'acomp'
plot3D(x, parts=1:min(ncol(X),4),...,
lwd=2, axis.col="gray", add=FALSE, cex=2,
vlabs=colnames(x), vlabs.col=axis.col, center=FALSE,
scale=FALSE, log=FALSE, bbox=FALSE, axes=TRUE, size=cex,col=1)
## S3 method for class 'rcomp'
plot3D(x,parts=1:min(ncol(X),4),...,
lwd=2,axis.col="gray",add=FALSE,cex=2,
vlabs=colnames(x),vlabs.col=axis.col,center=FALSE,
scale=FALSE,log=FALSE,bbox=FALSE,axes=TRUE,size=cex,col=1)

Arguments
x 
an aplus object to be plotted 
parts 
a numeric xor character vector of length 3 coding the columns to be plotted 
... 
additional plotting parameters as described in

add 
logical, adding or new plot 
cex 
size of the plotting symbols 
lwd 
line width 
axis.col 
color of the axis 
vlabs 
the column names to be plotted, if missing defaults to the column names of the selected columns of X 
vlabs.col 
color of the labels 
center 
logical, should the data be centered 
scale 
logical, should the data be scaled 
log 
logical, indicating wether to plot in log scale 
bbox 
logical, whether to add a bounding box 
axes 
logical, whether plot a coordinate cross 
size 
size of the plotting symbols 
col 
the color used for dots, defaults to black. 
Details
The routine behaves different when 3 or four components should be
plotted. In case of four components:
If log is TRUE the data is plotted in ilr
coordinates. This is the isometric view of the data.
If log is FALSE the data is plotted in ipt
coordinates
and a tetrahedron is plotted around it if coors == TRUE
. This
can be used to do a tetrahedron plot.
In case of three components:
If log is TRUE the data is plotted in clr
coordinates. This can be used to visualize the clr plane.
If log is FALSE the data is plotted as is, showing the embedding of
the
threepart simplex in the threedimensional space.
In all cases:
If coors
is true, coordinate arrows are plotted
of length 1 in the origin of the space, except in the tetrahedron case.
Value
Called for its side effect of a 3D plot of an acomp object in an rgl plot.
Note
The function kingTetrahedron
provides an alternate way of
tetrahedron plots, based on a more advanced viewer, which must
be downloaded separately.
Author(s)
K.Gerald v.d. Boogaart http://www.stat.boogaart.de
See Also
kingTetrahedron
points3d
, plot3D
,
plot
, plot3D.rmult
,
plot3D.acomp
,plot3D.rcomp
,,
plot3D.aplus
,plot3D.rplus
Examples
1 2 3 4 5  data(SimulatedAmounts)
plot3D(acomp(sa.lognormals5),1:3,col="green")
plot3D(acomp(sa.lognormals5),1:3,log=TRUE,col="green")
plot3D(acomp(sa.lognormals5),1:4,col="green")
plot3D(acomp(sa.lognormals5),1:4,log=TRUE,col="green")

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 acomp: Aitchison compositions
 acomp: Aitchison compositions
 acomparith: Power transform in the simplex
 acomparith: Power transform in the simplex
 acompmargin: Marginal compositions in Aitchison Compositions
 acompmargin: Marginal compositions in Aitchison Compositions
 Activity10: Activity patterns of a statistician for 20 days
 Activity10: Activity patterns of a statistician for 20 days
 Activity31: Activity patterns of a statistician for 20 days
 Activity31: Activity patterns of a statistician for 20 days
 alr: Additive log ratio transform
 alr: Additive log ratio transform
 AnimalVegetation: Animal and vegetation measurement
 AnimalVegetation: Animal and vegetation measurement
 aplus: Amounts analysed in logscale
 aplus: Amounts analysed in logscale
 aplusarithm: vectorial arithmetic for data sets with aplus class
 apt: Additive planar transform
 apt: Additive planar transform
 ArcticLake: Artic lake sediment samples of different water depth
 ArcticLake: Artic lake sediment samples of different water depth
 arrows3d: arrows in 3D, based on package rgl
 arrows3d: arrows in 3D, based on package rgl
 asdataframe: Convert "compositions" classes to data frames
 asdataframe: Convert "compositions" classes to data frames
 axis3d: Drawing a 3D coordiante system to a plot, based on package...
 axis3d: Drawing a 3D coordiante system to a plot, based on package...
 balancebase: Compute balances for a compositional dataset.
 balancebase: Compute balances for a compositional dataset.
 barplot: Bar charts of amounts
 barplot: Bar charts of amounts
 Bayesite: Permeabilities of bayesite
 Bayesite: Permeabilities of bayesite
 binary: Treating binary and gadic numbers
 binary: Treating binary and gadic numbers
 biplot3d: Threedimensional biplots, based on package rgl
 biplot3d: Threedimensional biplots, based on package rgl
 Blood23: Blood samples
 Blood23: Blood samples
 Boxite: Compositions and depth of 25 specimens of boxite
 Boxite: Compositions and depth of 25 specimens of boxite
 boxplot: Displaying compositions and amounts with boxplots
 boxplot: Displaying compositions and amounts with boxplots
 ccomp: Count compositions
 ccomp: Count compositions
 ccompgof: Compositional Goodness of fit test
 ccompgof: Compositional Goodness of fit test
 cdt: Centered default transform
 cdt: Centered default transform
 ClamEast: Colorsize compositions of 20 clam colonies from East Bay
 ClamEast: Colorsize compositions of 20 clam colonies from East Bay
 ClamWest: Colorsize compositions of 20 clam colonies from West Bay
 ClamWest: Colorsize compositions of 20 clam colonies from West Bay
 clo: Closure of a composition
 clo: Closure of a composition
 clr: Centered log ratio transform
 clr: Centered log ratio transform
 clr2ilr: Convert between clr and ilr, and between cpt and ipt.
 clr2ilr: Convert between clr and ilr, and between cpt and ipt.
 clusterfinder: Heuristics to find subpopulations of outliers
 clusterfinder: Heuristics to find subpopulations of outliers
 codadendrogram: Dendrogram representation of acomp or rcomp objects
 codadendrogram: Dendrogram representation of acomp or rcomp objects
 coloredbiplot: A biplot providing somewhat easier access to details of the...
 coloredbiplot: A biplot providing somewhat easier access to details of the...
 colorsforoutliers: Create a color/char palette or for groups of outliers
 colorsforoutliers: Create a color/char palette or for groups of outliers
 CompLinModCo: Compositional Linear Model of Coregionalisation
 CompLinModCo: Compositional Linear Model of Coregionalisation
 compmiss: The policy of treatment of missing values in the...
 compmiss: The policy of treatment of missing values in the...
 compOKriging: Compositional Ordinary Kriging
 compOKriging: Compositional Ordinary Kriging
 compositions: library(compositions)
 compositions: library(compositions)
 ConfRadius: Helper to compute confidence ellipsoids
 ConfRadius: Helper to compute confidence ellipsoids
 cor: Correlations of amounts and compositions
 cor: Correlations of amounts and compositions
 Coxite: Compositions, depths and porosities of 25 specimens of coxite
 Coxite: Compositions, depths and porosities of 25 specimens of coxite
 cpt: Centered planar transform
 cpt: Centered planar transform
 DiagnosticProb: Diagnostic probabilities
 DiagnosticProb: Diagnostic probabilities
 dist: Distances in variouse approaches
 dist: Distances in variouse approaches
 ellipses: Draw ellipses
 ellipses: Draw ellipses
 endmemberCoordinates: Recast amounts as mixtures of endmembers
 endmemberCoordinates: Recast amounts as mixtures of endmembers
 Firework: Firework mixtures
 Firework: Firework mixtures
 fitdirichlet: Fitting a Dirichlet distribution
 fitdirichlet: Fitting a Dirichlet distribution
 fitsamemean: Fit Same Mean Different Variance Model
 fitsamemean: Fit Same Mean Different Variance Model
 gausstest: Classical Gauss Test
 gausstest: Classical Gauss Test
 geometricmean: The geometric mean
 geometricmean: The geometric mean
 getdetectionlimit: Gets the detection limit stored in the data set
 getdetectionlimit: Gets the detection limit stored in the data set
 Glacial: Compositions and total pebble counts of 92 glacial tills
 Glacial: Compositions and total pebble counts of 92 glacial tills
 goftests: Compositional Goodness of fit test
 goftests: Compositional Goodness of fit test
 groupparts: Group amounts of parts
 groupparts: Group amounts of parts
 gsiadd: Internal functions: Parallel operations of single and...
 gsiadd: Internal functions: Parallel operations of single and...
 gsiaddclass: Internal function: give a derived subclass to an object
 gsiaddclass: Internal function: give a derived subclass to an object
 gsicall: Internal functions of the compositions package
 gsicall: Internal functions of the compositions package
 gsiclosespread: Internal functions of the compositions package
 gsiclosespread: Internal functions of the compositions package
 gsicoorinfo: Internal functions of the compositions package
 gsicoorinfo: Internal functions of the compositions package
 gsicsum: Internal function: row and column sums of matrices
 gsidiagExtract: Internal functions: Get the diagonal of a matrix
 gsidiagExtract: Internal functions: Get the diagonal of a matrix
 gsidiagGenerate: Internal functions: Generate a diagonal matrix
 gsidiagGenerate: Internal functions: Generate a diagonal matrix
 gsidrop: Internal functions: A conditional drop
 gsidrop: Internal functions: A conditional drop
 gsieps: Internal variable: Negligible differences
 gsieps: Internal variable: Negligible differences
 gsieq: Internal function: Checking equality of IEEE special numbers
 gsieq: Internal function: Checking equality of IEEE special numbers
 gsiexpandrcomp: Internal function: Scaling rcomp
 gsiexpandrcomp: Internal function: Scaling rcomp
 gsifiltercall: Calling from a function with the own parameters
 gsifiltercall: Calling from a function with the own parameters
 gsigetbalstruct: An auxiliary functions to compute userdefined ilr and ipt...
 gsigetbalstruct: An auxiliary functions to compute userdefined ilr and ipt...
 gsigetD: Interal function: Get number of samples and number of parts...
 gsigetD: Interal function: Get number of samples and number of parts...
 gsiinternal: Environment containing the old gsi functions
 gsiinternal: Environment containing the old gsi functions
 gsiinvperm: Internal function: Invert a permutation
 gsiinvperm: Internal function: Invert a permutation
 gsiisSingleRow: Internal function: Can something be considered as a single...
 gsiisSingleRow: Internal function: Can something be considered as a single...
 gsimap01: Internal functions: Storing integers as reals
 gsimap01: Internal functions: Storing integers as reals
 gsimargin: Internal function: Compute a desired compositional margin
 gsimargin: Internal function: Compute a desired compositional margin
 gsimerge2signary: Auxiliary functions to compute userdefined ilr and ipt...
 gsimerge2signary: Auxiliary functions to compute userdefined ilr and ipt...
 gsipairrelativeMatrix: Internal functions of the compositions package
 gsipairrelativeMatrix: Internal functions of the compositions package
 gsipairs: Internal functions of the compositions package
 gsipairs: Internal functions of the compositions package
 gsiplain: Internal function: Convert to plain vector or matrix
 gsiplain: Internal function: Convert to plain vector or matrix
 gsiplotmargin: Internal functions of the compositions package
 gsiplotmargin: Internal functions of the compositions package
 gsiPrinBal: The canonical basis in the clr plane used for ilr and ipt...
 gsiPrinBal: The canonical basis in the clr plane used for ilr and ipt...
 gsirecode: Internal function: Recode missings with IEEE number and vice...
 gsirecode: Internal function: Recode missings with IEEE number and vice...
 gsireset3d: Internal functions of the compositions package
 gsisimshape: Internal function: Reshape an object to the shape type of...
 gsisimshape: Internal function: Reshape an object to the shape type of...
 gsispreadToIsoSpace: Internal functions of the compositions package
 gsispreadToIsoSpace: Internal functions of the compositions package
 gsisvdsolve: Internal function: Solves singular and non square equation...
 gsisvdsolve: Internal function: Solves singular and non square equation...
 gsitextpanel: Internal function: A panel displaying a label only
 gsitextpanel: Internal function: A panel displaying a label only
 gsivarwithlosts: Internal function: computes variance of compositional data...
 gsivarwithlosts: Internal function: computes variance of compositional data...
 Hongite: Compositions of 25 specimens of hongite
 Hongite: Compositions of 25 specimens of hongite
 HotellingsTsq: Hotellings T square distribution
 HotellingsTsq: Hotellings T square distribution
 HouseholdExp: Household Expenditures
 HouseholdExp: Household Expenditures
 Hydrochem: Hydrochemical composition data set of Llobregat river basin...
 Hydrochem: Hydrochemical composition data set of Llobregat river basin...
 idt: Isometric default transform
 idt: Isometric default transform
 iit: Isometric identity transform
 iit: Isometric identity transform
 ilr: Isometric log ratio transform
 ilr: Isometric log ratio transform
 ilrBase: The canonical basis in the clr plane used for ilr and ipt...
 ilrBase: The canonical basis in the clr plane used for ilr and ipt...
 ilt: Isometric log transform
 ilt: Isometric log transform
 ipt: Isometric planar transform
 ipt: Isometric planar transform
 isAcomp: Check for compositional data type
 isAcomp: Check for compositional data type
 ismahalanobisoutlier: Checking for outliers
 ismahalanobisoutlier: Checking for outliers
 isoportion: Isoportion and Isoproportionlines
 isoportion: Isoportion and Isoproportionlines
 jura: The jura dataset
 jura: The jura dataset
 kingtetrahedron: Ploting composition into rotable tetrahedron
 kingtetrahedron: Ploting composition into rotable tetrahedron
 Kongite: Compositions of 25 specimens of kongite
 Kongite: Compositions of 25 specimens of kongite
 lines: Draws connected lines from point to point.
 lines: Draws connected lines from point to point.
 logratioVariogram: Empirical variograms for compositions
 logratioVariogram: Empirical variograms for compositions
 lrvgram: vgram2lrvgram
 lrvgram: vgram2lrvgram
 mahalanobisdist: Compute Mahalanobis distances based von robust Estimations
 matmult: inner product for matrices and vectors
 matmult: inner product for matrices and vectors
 matmultacomp: inner product for datasets with a vector space structure
 matmultacomp: inner product for datasets with a vector space structure
 meanAcomp: Mean amounts and mean compositions
 meanAcomp: Mean amounts and mean compositions
 meanrow: The arithmetic mean of rows or columns
 meanrow: The arithmetic mean of rows or columns
 Metabolites: Steroid metabolite patterns in adults and children
 Metabolites: Steroid metabolite patterns in adults and children
 missingProjector: Returns a projector the the observed space in case of...
 missingProjector: Returns a projector the the observed space in case of...
 missingsummary: Classify and summarize missing values in a dataset
 missingsummary: Classify and summarize missing values in a dataset
 mix2compositions: Transformations from 'mixtures' to 'compositions' classes
 mix2compositions: Transformations from 'mixtures' to 'compositions' classes
 mixRead: Reads a data file in a mixR format
 mixRead: Reads a data file in a mixR format
 mvar: Metric summary statistics of real, amount or compositional...
 mvar: Metric summary statistics of real, amount or compositional...
 names: The names of the parts
 names: The names of the parts
 norm: Vector space norm
 norm: Vector space norm
 normalize: Normalize vectors to norm 1
 normalize: Normalize vectors to norm 1
 oneOrDataset: Treating single compositions as onerow datasets
 oneOrDataset: Treating single compositions as onerow datasets
 outlierclassifier: Detect and classify compositional outliers.
 outlierclassifier: Detect and classify compositional outliers.
 outlierplot: Plot various graphics to analyse outliers.
 outlierplot: Plot various graphics to analyse outliers.
 outliers: Analysing outliers in compositions.
 outliers: Analysing outliers in compositions.
 pairwisePlot: Creates a paneled plot like pairs for two different datasets.
 pairwisePlot: Creates a paneled plot like pairs for two different datasets.
 parametricMat: Unique parametrisations for matrices.
 parametricMat: Unique parametrisations for matrices.
 perturbe: Perturbation of compositions
 plot: Ternary diagrams
 plot: Ternary diagrams
 plot3d: plot in 3D based on rgl
 plot3d: plot in 3D based on rgl
 plot3dacomp: 3Dplot of compositional data
 plot3dacomp: 3Dplot of compositional data
 plot3daplus: 3Dplot of positive data
 plot3daplus: 3Dplot of positive data
 plot3drmult: plot in 3D based on rgl
 plot3drmult: plot in 3D based on rgl
 plot3drplus: plot in 3D based on rgl
 plot3drplus: plot in 3D based on rgl
 plotlogratioVariogram: Empirical variograms for compositions
 plotlogratioVariogram: Empirical variograms for compositions
 plotmissingsummary: Plot a Missing Summary
 plotmissingsummary: Plot a Missing Summary
 plotpos: Displaying amounts in scatterplots
 plotpos: Displaying amounts in scatterplots
 PogoJump: Honk Kong PogoJumps Championship
 PogoJump: Honk Kong PogoJumps Championship
 powerofmatrix: power transform of a matrix
 powerofmatrix: power transform of a matrix
 princompacomp: Principal component analysis for Aitchison compositions
 princompacomp: Principal component analysis for Aitchison compositions
 princompaplus: Principal component analysis for amounts in log geometry
 princompaplus: Principal component analysis for amounts in log geometry
 princomprcomp: Principal component analysis for real compositions
 princomprcomp: Principal component analysis for real compositions
 princomprmult: Principal component analysis for real data
 princomprmult: Principal component analysis for real data
 princomprplus: Principal component analysis for real amounts
 princomprplus: Principal component analysis for real amounts
 print: Printing compositional data.
 print: Printing compositional data.
 pwlrPlot: Plots of pairwise logratio against a covariable.
 pwlrPlot: Plots of pairwise logratio against a covariable.
 qqnorm: Normal quantile plots for compositions and amounts
 qqnorm: Normal quantile plots for compositions and amounts
 R2: R square
 R2: R square
 raitchison: Aitchison Distribution
 raitchison: Aitchison Distribution
 ratioLoadings: Loadings of relations of two amounts
 ratioLoadings: Loadings of relations of two amounts
 rcomp: Compositions as elements of the simplex embedded in the...
 rcomp: Compositions as elements of the simplex embedded in the...
 rcomparithm: Arithmetic operations for compositions in a real geometry
 rcomparithm: Arithmetic operations for compositions in a real geometry
 rcompmargin: Marginal compositions in real geometry
 rcompmargin: Marginal compositions in real geometry
 rDirichlet: Dirichlet distribution
 rDirichlet: Dirichlet distribution
 readgeoeas: Reads a data file in a geoeas format
 readgeoeas: Reads a data file in a geoeas format
 replot: Modify parameters of compositional plots.
 replot: Modify parameters of compositional plots.
 rlnorm: The multivariate lognormal distribution
 rlnorm: The multivariate lognormal distribution
 rmahalanobis: Compute distributions of empirical Mahalanobis distances...
 rmahalanobis: Compute distributions of empirical Mahalanobis distances...
 rmult: Simple treatment of real vectors
 rmult: Simple treatment of real vectors
 rmultarithm: vectorial arithmetic for datasets in a classical vector scale
 rmultarithm: vectorial arithmetic for datasets in a classical vector scale
 rmultmatmult: inner product for datasets with vector scale
 rmultmatmult: inner product for datasets with vector scale
 rnorm: Normal distributions on special spaces
 rnorm: Normal distributions on special spaces
 robustness: Handling robustness issues and outliers in compositions.
 robustness: Handling robustness issues and outliers in compositions.
 rplus: Amounts i.e. positive numbers analysed as objects of the real...
 rplus: Amounts i.e. positive numbers analysed as objects of the real...
 rplusarithm: vectorial arithmetic for data sets with rplus class
 rplusarithm: vectorial arithmetic for data sets with rplus class
 rpois: Simulate count compositions without overdispersion
 rpois: Simulate count compositions without overdispersion
 runif: The uniform distribution on the simplex
 runif: The uniform distribution on the simplex
 scalar: Parallel scalar products
 scalar: Parallel scalar products
 scale: Normalizing datasets by centering and scaling
 scale: Normalizing datasets by centering and scaling
 Sediments: Proportions of sand, silt and clay in sediments specimens
 Sediments: Proportions of sand, silt and clay in sediments specimens
 segments: Draws straight lines from point to point.
 segments: Draws straight lines from point to point.
 SerumProtein: Serum Protein compositions of blood samples
 SerumProtein: Serum Protein compositions of blood samples
 ShiftOperators: Shifts of machine operators
 ShiftOperators: Shifts of machine operators
 simplemissingplot: Ternary diagrams
 simplemissingplot: Ternary diagrams
 SimulatedAmounts: Simulated amount datasets
 SimulatedAmounts: Simulated amount datasets
 simulatemissing: Artifical simulation of various kinds of missings/polluted...
 simulatemissing: Artifical simulation of various kinds of missings/polluted...
 Skulls: Measurement of skulls
 Skulls: Measurement of skulls
 SkyeAFM: AFM compositions of 23 aphyric Skye lavas
 SkyeAFM: AFM compositions of 23 aphyric Skye lavas
 split: Splitting datasets in groups given by factors
 straight: Draws straight lines.
 straight: Draws straight lines.
 summaryAcomp: Summarizing a compositional dataset in terms of ratios
 summaryAcomp: Summarizing a compositional dataset in terms of ratios
 summaryAplus: Summaries of amounts
 summaryAplus: Summaries of amounts
 summaryRcomp: Summary of compositions in real geometry
 summaryRcomp: Summary of compositions in real geometry
 sumprojector: Compute the global projector to the observed subspace.
 sumprojector: Compute the global projector to the observed subspace.
 Supervisor: Proportions of supervisor's statements assigned to different...
 Supervisor: Proportions of supervisor's statements assigned to different...
 ternaryAxis: Axis for ternary diagrams
 ternaryAxis: Axis for ternary diagrams
 tests: Compositional Goodness of fit test
 tests: Compositional Goodness of fit test
 totals: Total sum of amounts
 totals: Total sum of amounts
 tryDebugger: Empirical variograms for compositions
 ult: Uncentered log transform
 ult: Uncentered log transform
 varAcomp: Variances and covariances of amounts and compositions
 varAcomp: Variances and covariances of amounts and compositions
 variation: Variation matrices of amounts and compositions
 variation: Variation matrices of amounts and compositions
 variograms: Variogram functions
 variograms: Variogram functions
 varmlm: Residual variance of a model
 varmlm: Residual variance of a model
 vcovAcomp: Variance covariance matrix of parameters in compositional...
 vcovAcomp: Variance covariance matrix of parameters in compositional...
 vgmFit: Compositional variogram model fitting
 vgmFit: Compositional variogram model fitting
 WhiteCells: Whitecell composition of 30 blood samples by two different...
 WhiteCells: Whitecell composition of 30 blood samples by two different...
 Yatquat: Yatquat fruit evaluation
 Yatquat: Yatquat fruit evaluation
 zeroreplace: Zeroreplacement routine
 zeroreplace: Zeroreplacement routine