gstudio

An R package for the spatial analysis of population genetic marker data, including population graph construction, genetic diversity and structure estimation, directional gene flow analysis, and interactive visualization.

For complete documentation see: http://dyerlab.github.io/gstudio/

Installation

remotes::install_github("dyerlab/gstudio")

Tidy data philosophy

All analysis functions return standard data.frame objects that plug directly into ggplot2. The package does not wrap ggplot2 internally — you get the data back and plot it yourself. Population graphs are visualized with the ggraph package.

library(gstudio)
library(ggplot2)
data(arapat)

# Allele frequencies → hand off to ggplot
frequencies(arapat, loci = "LTRS", stratum = "Species") |>
  ggplot(aes(x = Allele, y = Frequency, fill = Stratum)) +
  geom_bar(stat = "identity", position = "dodge") +
  theme_minimal()

Key functions

Locus data

• locus() / as.locus() — create diploid locus objects from various input formats
• frequencies() — tidy allele frequency table (zero-fills missing allele/stratum combinations when stratum= is supplied)
• genetic_diversity() — per-locus diversity statistics (He, Ho, Ae, Fis, …)
• genetic_distance() — pairwise distance matrices (AMOVA, Euclidean, Nei, cGD, …)
• genetic_structure() — Gst, Gst′, Dest, Fst

Population graphs

• population_graph(data, stratum) — build a conditional-independence graph from multilocus data
• decorate_graph(graph, data, stratum) — attach data frame columns as vertex attributes
• asymmetric_weights(graph) — tSNE-inspired directional edge weights; returns a tidy data frame with dij, dji, and Delta per edge
• asymmetric_popgraph(graph) — convert an undirected popgraph to a directed one using the asymmetric weights

Interactive maps

• strata_coordinates(data) — population centroid data frame (Stratum, Longitude, Latitude)
• addAlleleFrequencies(map, freqs) — add allele-frequency pie charts to a leaflet map following the pipe convention:

library(leaflet)
library(leaflet.minicharts)

freqs <- frequencies(arapat, loci = "LTRS", stratum = "Species")

strata_coordinates(arapat, stratum = "Species") |>
  leaflet() |>
  addTiles() |>
  addAlleleFrequencies(freqs)

Simulation

• simulate_pop() / make_population() / mate() / migrate() — forward-time individual-based simulation

I/O

• read_population() / write_population() — read/write genotype data
• to_sf() — convert popgraph nodes or edges to an sf spatial object
• to_genepop() / to_structure() / to_json() — export to common formats

Deprecated

• to_SpatialPoints() / to_SpatialLines() — use to_sf() instead (sp package superseded by sf)

Contributing

Questions, bug reports, and contributions welcome. Contact Rodney J. Dyer or visit http://dyerlab.org