biplot.gmd: The GMD-biplot

In taryue/GMDecomp: Visualization tools for the Generalized Matrix Decomposition (GMD).

Description

Biplots based on generelized matrix decomposition.

Usage

## S3 method for class 'gmd'
biplot(x, ...)

Arguments

x	An object of class "gmd" that is the output from GMD.
...	Optional arguments (see Details).

Details

The optional arguments that can be passed in the biplot are

• index a numeric vector specifying which variables(arrows) to display. The default is to plot the three longest arrows.

• names a string vector specifying the names of the arrows. The default name of the i-th variable is Vi.

• sample.col The color of the sample dots. The default is grey.

• sample.pch Either an integer specifying a symbol or a single character to be used in plotting sample points. The default is 19.

• arrow.col The color of the arrows. The default is orange.

• arrow.cex A numeric value giving the size of the labels of the arrows. The default is 1.

Author(s)

Parker Knight and Yue Wang [e-mail]

References

Yue Wang, Timothy Randolph, Ali Shojaie and Jing Ma (2019). The GMD-biplot and its application to microbiome data.

See Also

GMD, screeplot.gmd

Examples

## Not run: 
   X = matrix(rnorm(1000), 50, 20)
   autocorr.mat <- function(p, rho) {
     mat <- diag(p)
     return(rho^abs(row(mat)-col(mat)))
     }
   H = autocorr.mat(50, 0.6)
   Q = autocorr.mat(20, 0.7)
   GMD.fit = GMD(X, H, Q, 2)
   screeplot(GMD.fit)
   biplot(GMD.fit)
   
## End(Not run)

taryue/GMDecomp documentation built on Nov. 5, 2019, 10 a.m.