R/plot_reefish_survey.R

In Grelot/geogendivr: Geographic Gene Diversity in R

library(sp)
library(rnaturalearth)
library(rnaturalearthdata)
library(tidyverse)
library(geosphere)
library(rgeos)

#' @export
plot_reefish_survey <- function (reefishSurveyEnvSocio, clusterDistanceThreshold=500) {
  world <- rnaturalearth::ne_countries(scale = "medium", returnclass = "sf")
  coords <- data.frame(lon = reefishSurveyEnvSocio$SiteLongitude,
                       lat = reefishSurveyEnvSocio$SiteLatitude)
  # convert data to a SpatialPointsDataFrame object
  xy <- sp::SpatialPointsDataFrame(
    coords, data.frame(ID=seq(1:length(coords$lon))),
    proj4string=sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84"))
  # use the distm function to generate a geodesic distance matrix in meters
  mdist <- geosphere::distm(xy)
  # cluster all points using a hierarchical clustering approach
  hc <- hclust(as.dist(mdist), method="complete")
  # define the distance threshold, in this case 500,000 m
  d=clusterDistanceThreshold*1000
  # define clusters based on a tree "height" cutoff "d" and add them to the SpDataFrame
  xy$clust <- cutree(hc, h=d)
  ## centroid
  cent <- matrix(ncol=3, nrow=max(xy$clust))
  for (i in 1:max(xy$clust)) {
    # gCentroid from the rgeos package
    cent[i,c(1,2)] <- rgeos::gCentroid(subset(xy, clust == i))@coords
    cent[i,3] <- length(which(xy$clust == i))
  }
  ## dataframe to plot
  dfc <- data.frame(longitude=cent[,1],
                    latitude=cent[,2],
                    numberOfSurveys= cent[,3]
                    )
  ## plot world map and centroids surveys
  gg <- ggplot2::ggplot(data=world)+
        ggplot2::geom_sf()+
        ggplot2::geom_point(data = dfc, 
                            ggplot2::aes(x = longitude,
                                y = latitude,
                                color=numberOfSurveys
                               ), size = 2)+
        ggplot2::scale_color_gradient(low = 'yellow',  high = 'red')+
        ggplot2::theme(panel.grid.major = ggplot2::element_blank(),
                       panel.grid.minor = ggplot2::element_blank(),
                       panel.background = ggplot2::element_rect(fill = "lightblue",
                                                      colour = "lightblue")
                       )
  return(gg)
}