Geo-biodiversity profile distribution map

Plotting diversity profiles on a map. The genetic diversity profiles can be calculated using HierDq or HierDq_genlind function.

ggDivgeomap(data,x,y, scale = "medium", returnclass = "sf", 
size, title = "Global Genetic Diversity Map", 
subtitle = ("Scaled relative genetic diversity of HGDP populations"), ...)

Arguments

data	The dataframe contains the longitude, latitude, and the geographic coordinates of the location.
x	The longitude of the location.
y	The latitude of the location.
scale	scale of map to return, one of 110, 50, 10 or 'small', 'medium', 'large'
returnclass	'sp' default or 'sf' for Simple Features
size	The point size used to indicate the (relative) diversity.
title	Tittle of the plot, text.
subtitle	Subtitle of the plot
...	Aesthetic passing to ggplot

Details

There are four ways of plotting geographic map in this package. "ggDiversity" uses ggplot2 and rnaturalearth.

Value

A geographic map with points (size indicates diversity value) and densities.

References

Wickham, H. (2011). ggplot2. Wiley Interdisciplinary Reviews: Computational Statistics, 3(2), 180-185.

South, A. (2017). Rnaturalearth: world map data from natural earth. R package version 0.1. 0.

Qin, X. (2019). HierDpart: partitioning hierarchical diversity and differentiation across metrics and scales, from genes to ecosystems. R package version 0.5. 0 https://cran.r-project.org/package=HierDpart.

Author

qinxinghu@gmail.com

Examples

#Load data
data(Dprofile)
##plot
ggDivgeomap(data = Dprofile,x=Dprofile$Longitude, y= Dprofile$Latitude,
scale = "medium", returnclass = "sf",size=normalize(Dprofile$Dq1)*10,
title="Human Population Genetic Diversity Map",
subtitle=("Scaled relative genetic diversity of HGDP populations"))