R/pies_on_map.R

In dyerlab/gstudio: Tools Related to the Spatial Analysis of Genetic Marker Data

#' Create a pie chart map of allele frequencies on google maps.
#' 
#' This function takes a data.frame and makes a set of pie charts for allele frequencies 
#' @param x An object of type \code{data.frame} containing \code{locus} objects.
#' @param stratum The stratum to use for calculating frequencies (default 'Population')
#' @param locus The name of the locus to use (required)
#' @param longitude The name of the Longitude data column (default 'Longitude')
#' @param latitude The name of the Latitude data column (default 'Latitude')
#' @param max.rad The maximum radius size for the pie charts (in real space) as meters.  By 
#'  default, it takes the maximum distance between stratum divided by 50.  They do not change
#'  by zooming in and out, so you can 'tune' it in here.
#' @param ... Additional arguments to plotGoogleMaps function.
#' @return Nothing
#' # @importFrom plotGoogleMaps pieSP plotGoogleMaps
#' # @importFrom ggmap has_google_key google_key
#' # @importFrom sp SpatialPointsDataFrame proj4string<- CRS
#' ##############################################################    @export
#' @author Rodney J. Dyer \email{rjdyer@@vcu.edu}
#' @examples 
#' \dontrun{
#' data(arapat)
#' pies_on_map(arapat,locus="LTRS")
#' }
#' 
#' 
# pies_on_map <- function( x, stratum="Population", locus=NULL, longitude='Longitude',latitude='Latitude', max.rad=NULL, ...) {
#   if( !is(x,"data.frame"))
#     stop("Please pass a data frame to the pies_on_map() function.")
#   if( is.null(locus) || !(locus %in% names(x)))
#     stop("You must specify a locus to use in the analysis")
#   if( !(longitude %in% names(x)) || !(latitude %in% names(x)))
#     stop("You must specify the columns representing latitude and longitude in the data.frame")
#   if( !(stratum %in% names(x))) 
#     stop("You must specify a population column in the data.frame to use for coordinates")
#   
#   
#   if( !has_google_key() ) {
#     stop("To use the Google Javascript API, you must have an API key.  See ?ggmap::register_google for more information.")
#   }
#   
#   pts <- strata_coordinates(x,stratum=stratum,longitude=longitude,latitude=latitude,as.SpatialPoints = TRUE)
#   freqs <- frequency_matrix(x,stratum=stratum,loci=locus)
#   col_names <- names(freqs)[2:ncol(freqs)]
#   
#   data <- SpatialPointsDataFrame( pts, freqs)
#   proj4string(data) <- CRS('+init=epsg:4326')
#   
#   
#   if( is.null( max.rad) ) {
#     d <- strata_distance(strata_coordinates(x,stratum=stratum,longitude=longitude,latitude=latitude))
#     max.rad <- max(d)/50*1000
#   }
#   
#   pies <- pieSP(data,zcol=col_names,max.radius=max.rad)
#   pies$allele <- rep(col_names,nrow(freqs))
#   
#   
#   api <- paste( "https://maps.googleapis.com/maps/api/js?key=",
#                 google_key(),
#                 "&callback=initMap", sep="" )
#   
#   m <- plotGoogleMaps(pies,zcol='allele', api=api, ...)
#   invisible(NULL)
#   
# }