View source: R/export_to_mvmapper.R
export_to_mvmapper | R Documentation |
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, ...) ## 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, ...)
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
|
mvmapper
can be found at:
https://popphylotools.github.io/mvMapper/
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
.
Thibaut Jombart thibautjombart@gmail.com
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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