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.
export_to_mvmapper(x, ...)# S3 method for default
export_to_mvmapper(x, ...)
# S3 method for dapc
export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
# S3 method for dudi
export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
# S3 method for spca
export_to_mvmapper(x, info, write_file = TRUE, out_file = NULL, ...)
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 follow PC1.
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) for assigned_grp.
The analysis to be exported. Can be a dapc, spca, or a
dudi object.
Further arguments to pass to other methods.
A data.frame with additional information containing at
least the following columns: key (unique individual identifier),
lat (latitude), and lon (longitude). Other columns will be
exported as well, but are optional.
A logical indicating if the output should be written
out to a .csv file. Defaults to TRUE.
A character string indicating the file to which the output
should be written. If NULL, the file used will be named
'mvmapper_data_[date and time].csv'
Thibaut Jombart thibautjombart@gmail.com
mvmapper can be found at:
https://popphylotools.github.io/mvMapper/
mvmapper is available at:
https://popphylotools.github.io/mvMapper/
# 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)
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