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**compositions**: Compositional Data Analysis**coloredbiplot**: A biplot providing somewhat easier access to details of the...

# A biplot providing somewhat easier access to details of the plot.

### Description

This function generates a simple biplot out of various source and allows to color the objects individually. (Warning: This preliminary version is likely to be changed in next edition)

### Usage

1 2 3 4 5 6 7 8 9 10 11 12 | ```
## Default S3 method:
coloredBiplot(x, y, var.axes = TRUE, col,
cex = rep(par("cex"), 2), xlabs = NULL, ylabs = NULL, expand=1,
xlim = NULL, ylim = NULL, arrow.len = 0.1, main = NULL, sub = NULL,
xlab = NULL, ylab = NULL, xlabs.col = NULL, xlabs.pc=NULL, ...)
## S3 method for class 'princomp'
coloredBiplot(x, choices = 1:2, scale = 1,
pc.biplot=FALSE, ...)
## S3 method for class 'prcomp'
coloredBiplot(x, choices = 1:2, scale = 1,
pc.biplot=FALSE, ...)
``` |

### Arguments

`x` |
a representation of the the co-information to be plotted, given by a result of princomp or prcomp; or the first set of coordinates to be plotted |

`y` |
optional, the second set of coordinates to be potted |

`var.axes` |
If 'TRUE# the second set of points have arrows representing them as (unscaled) axes. |

`col` |
One color (to be used for the y set) or a vector of two colors (to be used for x and y sets respectively, if xlabs.col is NULL) |

`cex` |
the usual cex parameter for plotting; can be a length-2 vector to format differently x and y labels/symbols. |

`xlabs` |
The names to write for the points of the first set |

`ylabs` |
The names to write for the points of the second set |

`expand` |
An expansion factor to apply when plotting the second set of points relative to the first. This can be used to tweak the scaling of the two sets to a physically comparable scale. |

`xlim` |
horizontal axis limits |

`ylim` |
vertical axis limits |

`arrow.len` |
The length of the arrow heads on the axes plotted in 'var.axes' is true. The arrow head can be suppressed by 'arrow.len=0'. |

`main` |
main title |

`sub` |
subtitle |

`xlab` |
horizontal axis title |

`ylab` |
vertical axis title |

`xlabs.col` |
The color(s) to draw the points of the first set |

`xlabs.pc` |
the plotting character(s) for the first set |

`scale` |
the way to distribute the singular values on the
right or left singular vectors for princomp and prcomp objects
(see |

`choices` |
the components to be plotted (see |

`pc.biplot` |
should be scaled by |

`...` |
further parameters for plot |

### Details

The functions is provided for convenience.

### Value

The function is called only for the side effect of plotting. It is a modification of the standard R routine 'biplot'.

### Author(s)

Raimon Tolosana-Delgado, K.Gerald v.d. Boogaart http://www.stat.boogaart.de

### See Also

`biplot`

, `plot.acomp`

### Examples

1 2 3 | ```
data(SimulatedAmounts)
coloredBiplot(x=princomp(acomp(sa.outliers5)),pc.biplot=FALSE,
xlabs.pc=c(1,2,3), xlabs.col=2:4, col="black")
``` |

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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 log-scale
- aplus: Amounts analysed in log-scale
- 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 g-adic numbers
- binary: Treating binary and g-adic numbers
- biplot3d: Three-dimensional biplots, based on package rgl
- biplot3d: Three-dimensional 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 box-plots
- boxplot: Displaying compositions and amounts with box-plots
- 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: Color-size compositions of 20 clam colonies from East Bay
- ClamEast: Color-size compositions of 20 clam colonies from East Bay
- ClamWest: Color-size compositions of 20 clam colonies from West Bay
- ClamWest: Color-size 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 end-members
- endmemberCoordinates: Recast amounts as mixtures of end-members
- 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 user-defined ilr and ipt...
- gsigetbalstruct: An auxiliary functions to compute user-defined 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 user-defined ilr and ipt...
- gsimerge2signary: Auxiliary functions to compute user-defined 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 Isoproportion-lines
- isoportion: Isoportion- and Isoproportion-lines
- 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 one-row datasets
- oneOrDataset: Treating single compositions as one-row 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: 3D-plot of compositional data
- plot3dacomp: 3D-plot of compositional data
- plot3daplus: 3D-plot of positive data
- plot3daplus: 3D-plot 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 Pogo-Jumps Championship
- PogoJump: Honk Kong Pogo-Jumps 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: White-cell composition of 30 blood samples by two different...
- WhiteCells: White-cell composition of 30 blood samples by two different...
- Yatquat: Yatquat fruit evaluation
- Yatquat: Yatquat fruit evaluation
- zeroreplace: Zero-replacement routine
- zeroreplace: Zero-replacement routine