export_to_mvmapper {adegenet} | R Documentation |
Export analysis for mvmapper visualisation
Description
mvmapper
is an interactive tool for visualising outputs of a
multivariate analysis on a map from a web browser. The function
export_to_mvmapper
is a generic with methods for several standard
classes of analyses in adegenet
and ade4
. Information on
individual locations, as well as any other relevant data, is passed through
the second argument info
. By default, the function returns a formatted
data.frame
and writes the output to a .csv file.
Usage
export_to_mvmapper(x, ...)
## Default S3 method:
export_to_mvmapper(x, ...)
## S3 method for class 'dapc'
export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
## S3 method for class 'dudi'
export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
## S3 method for class 'spca'
export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
Arguments
x |
The analysis to be exported. Can be a |
... |
Further arguments to pass to other methods. |
info |
A |
write_file |
A |
out_file |
A character string indicating the file to which the output
should be written. If NULL, the file used will be named
|
Details
mvmapper
can be found at:
https://popphylotools.github.io/mvMapper/
Value
A data.frame
which can serve as input to mvmapper
,
containing at least the following columns:
-
key
: unique individual identifiers -
PC1
: first principal component; further principal components are optional, but if provided will be numbered and followPC1
. -
lat
: latitude for each individual -
lon
: longitude for each individual
In addition, specific information is added for some analyses:
-
spca
:Lag_PC
columns contain the lag-vectors of the principal components; the lag operator computes, for each individual, the average score of neighbouring individuals; it is useful for clarifying patches and clines. -
dapc
:grp
is the group used in the analysis;assigned_grp
is the group assignment based on the discriminant functions;support
is the statistical support (i.e. assignment probability) forassigned_grp
.
Author(s)
Thibaut Jombart thibautjombart@gmail.com
See Also
mvmapper
is available at:
https://popphylotools.github.io/mvMapper/
Examples
# An example using the microsatellite dataset of Dupuis et al. 2016 (781
# individuals, 10 loci, doi: 10.1111/jeb.12931)
# Reading input file from adegenet
input_data <- system.file("data/swallowtails.rda", package="adegenet")
data(swallowtails)
# conducting a DAPC (n.pca determined using xvalDapc, see ??xvalDapc)
dapc1 <- dapc(swallowtails, n.pca=40, n.da=200)
# read in swallowtails_loc.csv, which contains "key", "lat", and "lon"
# columns with column headers (this example contains additional columns
# containing species identifications, locality descriptions, and COI
# haplotype clades)
input_locs <- system.file("files/swallowtails_loc.csv", package = "adegenet")
loc <- read.csv(input_locs, header = TRUE)
# generate mvmapper input file, automatically write the output to a csv, and
# name the output csv "mvMapper_Data.csv"
out_dir <- tempdir()
out_file <- file.path(out_dir, "mvMapper_Data.csv")
out <- export_to_mvmapper(dapc1, loc, write_file = TRUE, out_file = out_file)