gl.dist.ind {dartR.base} | R Documentation |
Calculates a distance matrix for individuals defined in a genlight object
Description
Calculates various distances between individuals based on allele frequencies or presence-absence data
Usage
gl.dist.ind(
x,
method = NULL,
scale = FALSE,
swap = FALSE,
type = "dist",
plot.display = TRUE,
plot.theme = theme_dartR(),
plot.colors = NULL,
plot.file = NULL,
plot.dir = NULL,
verbose = NULL
)
Arguments
x |
Name of the genlight [required]. |
method |
Specify distance measure [SNP: Euclidean; P/A: Simple]. |
scale |
If TRUE, the distances are scaled to fall in the range [0,1] [default TRUE] |
swap |
If TRUE and working with presence-absence data, then presence (no disrupting mutation) is scored as 0 and absence (presence of a disrupting mutation) is scored as 1 [default FALSE]. |
type |
Specify the type of output, dist or matrix [default dist] |
plot.display |
If TRUE, resultant plots are displayed in the plot window [default TRUE]. |
plot.theme |
Theme for the plot. See Details for options [default theme_dartR()]. |
plot.colors |
List of two color names for the borders and fill of the plots [default c("#2171B5","#6BAED6")]. |
plot.file |
Name for the RDS binary file to save (base name only, exclude extension) [default NULL] |
plot.dir |
Directory to save the plot RDS files [default as specified by the global working directory or tempdir()] |
verbose |
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]. |
Details
The distance measure for SNP genotypes can be one of:
Euclidean Distance [method = "Euclidean"]
Scaled Euclidean Distance [method='Euclidean", scale=TRUE]
Simple Mismatch Distance [method="Simple"]
Absolute Mismatch Distance [method="Absolute"]
Czekanowski (Manhattan) Distance [method="Manhattan"]
The distance measure for Sequence Tag Presence/Absence data (binary) can be one of:
Euclidean Distance [method = "Euclidean"]
Scaled Euclidean Distance [method='Euclidean", scale=TRUE]
Simple Matching Distance [method="Simple"]
Jaccard Distance [method="Jaccard"]
Bray-Curtis Distance [method="Bray-Curtis"]
Refer to the documentation of functions in https://doi.org/10.1101/2023.03.22.533737 for algorithms and definitions.
Value
An object of class 'matrix' or dist' giving distances between individuals
Author(s)
Author(s): Custodian: Arthur Georges – Post to #' https://groups.google.com/d/forum/dartr
See Also
Other distance:
gl.dist.pop()
,
gl.fdsim()
,
utils.dist.ind.snp()
Examples
D <- gl.dist.ind(testset.gl[1:20,], method='manhattan')
D <- gl.dist.ind(testset.gs[1:20,], method='Jaccard',swap=TRUE)
D <- gl.dist.ind(testset.gl[1:20,], method='euclidean',scale=TRUE)