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Mantel test for a set of correlation matrices

Source: R/pairs_mantel.R
pairs_mantel.Rd

[Stable]

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.

See also

mantel_test()

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
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()
# }