plotMatrix: Plot a Numerical Matrix
In ecbrown/LaplacesDemon: Complete Environment for Bayesian Inference

Description Usage Arguments Details Author(s) See Also Examples

This function plots a numerical matrix, and is often used to plot the following matrices: correlation, covariance, distance, and precision.

1 2	plotMatrix(x, col=colorRampPalette(c("red","black","green"))(100), cex=1, circle=TRUE, order=FALSE, zlim=NULL, title="", PDF=FALSE, ...)

`x`	This required argument is a numerical matrix, or an object of class `bayesfactor`, `demonoid`, `iterquad`, `laplace`, `pmc`, `posteriorchecks`, or `vb`. See more information below regarding these classes. One component of a blocked proposal covariance matrix must be pointed to explicitly, rather than to the object of class `demonoid`.
`col`	This argument specifies the colors of the circles. By default, the `colorRampPalette` function colors strong positive correlation as `green`, zero correlation as `black`, and strong negative correlation as `red`, and provides 100 color gradations.
`cex`	When `circle=TRUE`, this argument specifies the size of the marginal text, the names of the parameters or variables, and defaults to 1.
`circle`	Logical. When `TRUE`, each element in the numeric matrix is represented with a circle, and a larger circle is assigned to elements that are farther from zero. Also, when `TRUE`, the gradation scale does not appear to the right of the plot.
`order`	Logical. This argument defaults to `FALSE`, and presents the parameters or variables in the same order as in the numeric matrix. When `TRUE`, the parameters or variables are ordered using principal components analysis.
`zlim`	When `circle=FALSE`, the gradation scale may be constrained to an interval by `zlim`, such as `zlim=c(-1,1)`, and only values within the interval are plotted.
`title`	This argument specifies the title of the plot, and the default does not include a title. When `x` is of class `posteriorchecks`, the title is changed to `Posterior Correlation`.
`PDF`	Logical. When `TRUE`, the plot is saved as a .pdf file.
`...`	Additional arguments are unused.

The plotMatrix function produces one of two styles of plots, depending on the circle argument. A K x K numeric matrix of K parameters or variables is plotted. The plot is a matrix of the same dimensions, in which each element is colored (and sized, when circle=TRUE) according to its value.

Although plotMatrix does not provide the same detail as a numeric matrix, it is easier to discover elements of interest according to color (and size when circle=TRUE).

The plotMatrix function is not inherently Bayesian, and does not include uncertainty in matrices. Nonetheless, it is included because it is a useful graphical presentation of a numeric matrices, and is recommended to be used with the posterior correlation matrix in an object of class posteriorchecks.

When x is an object of class bayesfactor, matrix B is plotted. When x is an object of class demonoid (if it is a matrix), iterquad, laplace, pmc, or vb, the covariance matrix Covar is plotted. When x is an object of class posteriorchecks, the posterior correlation matrix is plotted.

This is a modified version of the circle.corr function of Taiyun Wei.

Taiyun Wei

PosteriorChecks

library(LaplacesDemon)
### Although it is most commonly used with an object of class
### posteriorchecks, it is applied here to a different correlation matrix.
data(mtcars)
plotMatrix(cor(mtcars), col=colorRampPalette(c("green","gray10","red"))(100),
     cex=1, circle=FALSE, order=TRUE)
plotMatrix(cor(mtcars), col=colorRampPalette(c("green","gray10","red"))(100),
     cex=1, circle=TRUE, order=TRUE)