pairs_mantel: Mantel test for a set of correlation matrices

In metan: Multi Environment Trials Analysis

Mantel test for a set of correlation matrices

Description

This function generate a pairwise matrix of plots to compare the similarity of two or more correlation matrices. In the upper diagonal are presented the plots and in the lower diagonal the result of Mantel test based on permutations.

Usage

pairs_mantel(
  ...,
  type = 1,
  nrepet = 1000,
  names = NULL,
  prob = 0.05,
  diag = FALSE,
  export = FALSE,
  main = "auto",
  file.type = "pdf",
  file.name = NULL,
  width = 8,
  height = 7,
  resolution = 300,
  size.point = 0.5,
  shape.point = 19,
  alpha.point = 1,
  fill.point = NULL,
  col.point = "black",
  minsize = 2,
  maxsize = 3,
  signcol = "green",
  alpha = 0.15,
  diagcol = "gray",
  col.up.panel = "gray",
  col.lw.panel = "gray",
  col.dia.panel = "gray",
  pan.spacing = 0.15,
  digits = 2
)

Arguments

...	The input matrices. May be an output generated by the function lpcor or a coerced list generated by the function as.lpcor
type	The type of correlation if an obect generated by the function lpcor is used. 1 = Linear correlation matrices, or 2 = partial correlation matrices.
nrepet	The number of permutations. Default is 1000
names	An optional vector of names of the same length of ... .
prob	The error probability for Mantel test.
diag	Logical argument. If TRUE, the Kernel density is shown in the diagonal of plot.
export	Logical argument. If TRUE, then the plot is exported to the current directory.
main	The title of the plot, set to 'auto'.
file.type	The format of the file if export = TRUE. Set to 'pdf'. Other possible values are *.tiff using file.type = 'tiff'.
file.name	The name of the plot when exported. Set to NULL, i.e., automatically.
width	The width of the plot, set to 8.
height	The height of the plot, set to 7.
resolution	The resolution of the plot if file.type = 'tiff' is used. Set to 300 (300 dpi).
size.point	The size of the points in the plot. Set to 0.5.
shape.point	The shape of the point, set to 19.
alpha.point	The value for transparency of the points: 1 = full color.
fill.point	The color to fill the points. Valid argument if points are between 21 and 25.
col.point	The color for the edge of the point, set to black.
minsize	The size of the letter that will represent the smallest correlation coefficient.
maxsize	The size of the letter that will represent the largest correlation coefficient.
signcol	The colour that indicate significant correlations (based on the prob value.), set to 'green'.
alpha	The value for transparency of the color informed in signcol, when 1 = full color. Set to 0.15.
diagcol	The color in the kernel distribution. Set to 'gray'.
col.up.panel, col.lw.panel, col.dia.panel	The color for the opper, lower and diagonal pannels. Set to 'gray', 'gray', and 'gray', respectively.
pan.spacing	The space between the pannels. Set to 0.15.
digits	The number of digits to show in the plot.

Value

An object of class gg, ggmatrix.

Author(s)

Tiago Olivoto [e-mail]

See Also

mantel_test()

Examples

library(metan)
# iris dataset
lpc <- iris %>%
       group_by(Species) %>%
       lpcor() %>%
       pairs_mantel(names = c('setosa', 'versicolor', 'virginica'))


# mtcars dataset
mt_num <- select_numeric_cols(mtcars)
lpdata <- as.lpcor(cor(mt_num[1:5]),
                   cor(mt_num[1:5]),
                   cor(mt_num[2:6]),
                   cor(mt_num[4:8])) %>%
          pairs_mantel()

metan documentation built on March 7, 2023, 5:34 p.m.