plot_assignment_dlr: Assignment plot of genotype likelihood.
In eriqande/assigner: Assignment Analysis with GBS/RADseq Data using R
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.
R Package Documentation
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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.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, |
strata |
(optional) A tab delimited file with 2 columns with header:
|
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 |
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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