Function reference • PopGenHelpR

All functions

Ancestry_barchart(): Plot an ancestry matrix for individuals and(or) populations.

Dif_Stats_Map(): WARNING! This function has been deprecated and is no longer supported. Please use the Network_map function. A function to map differentiation statistics.

Dif_stats(): WARNING! This function has been deprecated and is no longer supported. Please use the Differentiation function. A function to calculate differentiation statistics and perform significance testing with a vcf file.

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.

Div_Stats_Map(): WARNING! This function has been deprecated and is no longer supported. Please use the Point_map function instead. A function to map diversity statistics.

Div_stats(): WARNING! This function has been deprecated and is no longer supported. Please use the Heterozygosity and Private.alleles functions. A function to estimate heterozygosity and the number of private alleles from a vcf file.

Fst_dat: A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.

Het_dat: A data frame of hypothetical heterozygosity data produced by Div_Stats.

Heterozygosity(): A function to estimate seven measures of heterozygosity using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.

HornedLizard_Pop: A population assignment data frame to be used in Div_stats and Dif_stats.

HornedLizard_Pop: A vcfR object to be used in Div_stats and Dif_stats.

Network_map(): A function to map statistics (i.e., genetic differentiation) between points as a network on a map.

PCA(): A function to perform principal component analysis (PCA) on genetic data. Loci with missing data will be removed prior to PCA.

Pairwise_heatmap(): A function to plot a heatmap from a symmetric matrix.

Piechart_map(): Plot a map of ancestry pie charts.

Plot_ancestry(): WARNING! This function has been deprecated and is no longer supported. Please use the Ancestry_barchart and Piechart_map functions. Plot an ancestry matrix and map of ancestry pie charts.

Plot_coordinates(): A function to plot coordinates on a map.

Point_map(): A function to map statistics as colored points on a map.

Private.alleles(): A function to estimate the number of private alleles in each population.

Q_dat: A list representing a q-matrix and the locality information associated with the qmatrix