R/map_receptors.R

In dKvale/mnrisks2011: MNRISKS

#' map_receptors
#'
#' Map the average block group mnrisks results with leaflet
#' @param data The dataframe or sf object containing the modeling results for mapping.
#' @param result_col Column name containing the modeling concentration/risk results.
#' @param receptor_col Column name containing the receptor IDs.
#' @param colors Color palette to use for block group fill, ex. "viridis", "inferno", "Blues", "Greens"
#' @param reverse_colors Flip the color palette order
#' @param size Receptor or circle radius. Default = 5
#' @param signif_digits Number of significant figures to show in map labels
#' @keywords Map receptors mnrisks leaflet
#' @export
#' @examples
#' 
#' map_receptors(data = mnrisk_results,
#'               result_col = "cancer_risk",
#'               colors = "inferno")
# 

map_receptors <- function(data        = NULL,
                          result_col  = "cancer_risk",
                          receptor_col = "receptor",
                          colors      = "viridis",
                          reverse_colors = T,
                          size = 5,
                          signif_digits = 3) {
  
  # Test inputs ----
  if (is.null(data) | !"data.frame" %in% class(data)) stop("Incorrect data passed to function. Set `data` argument to the 'data.frame' or 'sf' object containing the modeling results.")
  
  if (!result_col %in% names(data)) stop(paste("The result_col [", result_col, "] was not found in the data."))
  
  if (!receptor_col %in% names(data)) stop(paste("The receptor_col [", receptor_col, "] was not found in the data."))
  
  # Set column names ----
  names(data)[grep(result_col, names(data))] <- "result"
  names(data)[grep(receptor_col, names(data))] <- "receptor"
  
  # Create color palette ----
  max_result <- max(data$result, na.rm = T)
  
  if (max_result < 1E-03) { 
    
    data$result <- data$result / 1E-05
    
    title_adj <- " per 100,000"
    
  } else {
    
    title_adj <- ""
    
  }
  
  max_result <- max(data$result, na.rm = T)
  
  pal <- colorNumeric(palette = colors, domain = data$result, reverse = reverse_colors)
  #pal <- leaflet::colorNumeric("viridis", quantile(data$result, c(seq(0,0.9,0.1),0.95,0.97,1)), reverse = T)
  
  
  # Create labels ----
  names(data) <- tolower(names(data))
  
  data$label <- paste0("<h1>Receptor #", data$receptor, "</h1>",
                       '<p style="font-size:14px; margin-top: -16px;">', result_col, "</p>",
                       "<h1 style='text-align: center; color: grey;'>", 
                       signif(data$result, signif_digits), title_adj, "</h1>")
  
  
  # Map the map ----
  leaflet(data %>% subset(!is.na(result))) %>%
    addProviderTiles(providers$CartoDB.Positron) %>%
    addCircleMarkers(color   = "darkgrey",
                     opacity = 0.3,
                     fillColor = ~pal(result),
                     fillOpacity = ~0.15*result/max_result + 0.3, # Scale the opacity up to 0.45 for highest risks
                     radius  = ~2*result/max_result + size,
                     label = ~lapply(label, htmltools::HTML),
                     stroke = T, 
                     weight = 1) %>%
    addLegend("bottomright", 
              pal = pal, 
              values = ~result, 
              title = paste0(result_col, title_adj),
              opacity = 0.7)
  
}