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Legacy POPMAPS 1.03 ancestry-surface visualization

Source: R/popmap_viz.R
popmap_viz.Rd

This function preserves the original POPMAPS plotting interface for compatibility with POPMAPS 1.03-era scripts. New analyses should use plot_popmaps() or write_popmaps_plot(), which provide terra-based map output, manuscript-style defaults, optional background rasters, and PNG export. popmap_viz() can draw hard boundaries only or hard boundaries with ancestry probabilities. Pie charts representing empirical ancestry patterns are drawn at sampling sites.

Usage

popmap_viz(
  pop_raster_list = "",
  input_locs = "",
  input_raster = "",
  maptype = c("bound", "ancestry"),
  pie_radius = 0.15,
  boundary_width = -0.015,
  crs = "+init=epsg:5070"
)

Arguments

pop_raster_list

An R object resulting from executing popmaps().

input_locs

An R object with rows as empirical sites and columns as: column 1, site name; column 2, decimal longitude or x-coordinate; column 3, decimal latitude or y-coordinate; columns 4 through n, ancestry coefficients for each genetic axis. The function depends on this precise column order; see the example data hija_struc.

input_raster

An R RasterLayer object defining the geographic extent for the spatial interpolation.

maptype

A string, either "bound" or "ancestry", that defines the map type. "bound" draws hard boundaries only. "ancestry" draws hard boundaries and the maximum ancestry-probability surface.

pie_radius

A numeric value modifying the size of the pie charts depicting empirical ancestry coefficients drawn on top of the probability surface.

boundary_width

Retained for compatibility with POPMAPS 1.03. Boundary buffering previously depended on retired spatial packages and is no longer applied.

crs

A string defining a mapping projection. The historical default is an Albers Equal Area Conic projection used by older POPMAPS examples.

References

Massatti R & Winkler DE. (2022) Spatially explicit management of genetic diversity using ancestry probability surfaces. Methods in Ecology and Evolution. http://dx.doi.org/10.1111/2041-210X.13902

Author

Rob Massatti

Examples

if (FALSE) { # \dontrun{
    ex_raster <- raster::aggregate(hija_raster,fact=16)  #Cells in embedded raster are aggregated to reduce computation time
    pp <- popmaps(input_raster=ex_raster,input_locs=hija_struc,empirical_pt_dist=5,num_sites=15,num_tested=4,popmod=-0.05,threshold=0,surface='G')
    popmap_viz(pop_raster_list=pp,input_locs=hija_struc,input_raster=ex_raster,maptype='ancestry',crs="+init=epsg:5070",boundary_width=-0.01)
} # }