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Ancestry_barchart()
- Plot an ancestry matrix for individuals and(or) populations.
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Differentiation()
- A function to estimate three measures of genetic differentiation using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.
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Fst_dat
- A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.
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Het_dat
- A data frame of hypothetical heterozygosity data produced by Heterozygosity.
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Heterozygosity()
- A function to estimate seven measures of heterozygosity using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.
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HornedLizard_Pop
- A population assignment data frame to be used in
Heterozygosity and Differentiation.
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HornedLizard_Pop
- A vcfR object to be used in
Heterozygosity and Differentiation.
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Network_map()
- A function to map statistics (i.e., genetic differentiation) between points as a network on a map.
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PCA()
- A function to perform principal component analysis (PCA) on genetic data. Loci with missing data will be removed prior to PCA.
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Pairwise_heatmap()
- A function to plot a heatmap from a symmetric matrix.
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Piechart_map()
- Plot a map of ancestry pie charts.
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Plot_coordinates()
- A function to plot coordinates on a map.
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Point_map()
- A function to map statistics as colored points on a map.
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Private.alleles()
- A function to estimate the number of private alleles in each population.
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Q_dat
- A list representing a q-matrix and the locality information associated with the qmatrix