plot_assignment_dlr: Assignment plot of genotype likelihood.

Description Arguments Value Author(s) References

Description

Create a figure similar to Paetkau's et al. (2004) Fig 6.

Arguments

data

The output assignment file (home likelihood or likelihood ratio statistics) from GENODIVE.

l.skip

(integer) The number of lines to skip before the individuals info in GenoDive assignment results (see Vignette).

number.individuals

(integer) The number of individuals analysed.

number.pop

(integer) The number of populations analysed.

pop.id.start

(Optional) The start of your population id in the name of your individual sample. Your individuals are identified in this form : SPECIES-POPULATION-MATURITY-YEAR-ID = CHI-QUE-ADU-2014-020, then, pop.id.start = 5. If you didn't name your individuals with the pop id in it, use the strata argument.

pop.id.end

(Optional) The end of your population id in the name of your individual sample. Your individuals are identified in this form : SPECIES-POPULATION-MATURITY-YEAR-ID = CHI-QUE-ADU-2014-020, then, pop.id.end = 7. If you didn't name your individuals with the pop id in it, use the strata argument.

strata

(optional) A tab delimited file with 2 columns with header: INDIVIDUALS and STRATA. Default: strata = NULL. The STRATA column is used here as the populations id of your sample.

pop.levels

A character string with your sampling sites or populations in the order you prefer (for tables and figure).

pop.labels

(optional) A character string for your populations labels. If you need to rename sampling sites in pop.levels or combined sites/pop into a different names, here is the place.

POPA

First population to compare.

POPB

Second population to compare (with A).

dlr

(optional) Character string with Dlr value.

x.dlr

(optional) Position to the x-axis of the Dlr value.

y.dlr

(optional) Position to the y-axis of the Dlr value.

fst

(optional) Character string with Fst value.

x.fst

(optional) Position to the x-axis of the Fst value.

y.fst

(optional) Position to the y-axis of the Fst value.

filename

(optional) Name of the figure written in the working directory.

plot.width

(optional) Width in cm of the figure.

plot.height

(optional) height in cm of the figure.

plot.dpi

(optional) Number of dpi for the figure (e.g 600).

Value

A list with the assignment table and the assignment plot.

Author(s)

Thierry Gosselin thierrygosselin@icloud.com

References

Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13, 55-65.

Meirmans PG, Van Tienderen PH (2004) genotype and genodive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794.


eriqande/assigner documentation built on May 16, 2019, 8:45 a.m.