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map_fun.R
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# functions for the leaflet map
# Create a data frame for colour-blind friendly LCM colour palette with the RGB values and class names
color_data_CB <- data.frame(
Class = c("Broadleaved woodland", "Coniferous woodland", "Arable", "Improved grassland", "Neutral grassland",
"Calcareous grassland", "Acid grassland", "Fen, Marsh and Swamp", "Heather and shrub",
"Heather grassland", "Bog", "Inland rock", "Saltwater", "Freshwater", "Supralittoral rock",
"Supralittoral sediment", "Littoral rock", "Littoral sediment", "Saltmarsh", "Urban", "Suburban"),
RGB = c("#3E3D32", "#004433", "#ECF2BD", "#FEAA73", "#DFE6EC", "#99C9DD", "#E9D6EC", "#76835C",
"#806480", "#B29278", "#9BB291", "#B3B3B3", "#000066", "#0000FF", "#B3B300", "#FFFFB3",
"#FFFF00", "#FFFF00", "#0080FF", "#000000", "#808080")
)
# rgb_vector <- as.character(color_data$RGB)
# class_vector <- as.character(color_data$Class)
#
# # Define legend colors and labels
# legend_colors <- color_data$RGB
# legend_labels <- color_data$Class
color_data <- data.frame(
Class = c("Broadleaved woodland", "Coniferous woodland", "Arable", "Improved grassland", "Neutral grassland",
"Calcareous grassland", "Acid grassland", "Fen, marsh and swamp", "Heather",
"Heather grassland", "Bog", "Inland rock", "Saltwater", "Freshwater", "Supralittoral rock",
"Supralittoral sediment", "Littoral rock", "Littoral sediment", "Saltmarsh", "Urban", "Suburban"),
RGB = c("#E10000", "#006600", "#732600", "#00ff00", "#7fe57f", "#70a800", "#998100", "#ffff00",
"#801a80", "#e68ca6", "#008073", "#d2d2ff", "#000080", "#0000FF", "#CCAA00", "#CCB300",
"#FFFF80", "#FFFF80", "#8080ff", "#000000", "#808080")
)
map_fun_EA_pollution <- function(map, data, label_IndustrySector = 'Industry sector',
fillColor = "blue",legend_title = 'EA Pollution Inventory 2021'){
map %>%
#addControl(data = data, html = paste("<h5>", Regulated_Industry_Sector, "</h5>", sep = ""), position = "topright") %>%
addCircleMarkers(
data = data,
lng = ~Longitude, lat = ~Latitude, radius = 8, #~radius,
popup = ~paste(
"<b>Substance Name: </b>", substance_name, "<br/>",
"<b>Quantity Released: </b>", quantity_released_tons, " tonnes<br/>",
"<b>Sector: </b>", Regulated_Industry_Sector, "<br/>",
"<b>Route: </b>", `ROUTE NAME`, "<br/>",
sep = ""
),
color = "black", # Outline color
fillColor = fillColor, # Fill color
fillOpacity = 0.8, # Opacity of the fill color
weight = 0.5,
group = legend_title
)
}
## TEST:data = data_process_EA_WQ_gcms()
## leaflet() %>% addTiles() %>% map_fun_EA_WQ_gcms(data=data)
map_fun_EA_WQ_gcms <- function(map, data, fillColor = "blue",
legend_title= 'EA water quality GCMS data'){
map %>%
#addControl(html = paste("<h5>", input$gcms_compound, " ", input$year_slider[1], " - ", input$year_slider[2], "</h5>", sep = ""), position = "topright") %>%
addCircleMarkers(
data = data,
lng = ~Longitude, lat = ~Latitude, radius = 8,# ~radius,
#clusterOptions = markerClusterOptions(maxClusterRadius=1),
popup = ~paste(
"<b>Sample Site ID: </b>", Sample_Site_ID, "<br/>",
"<b>Compound Name: </b>", Compound_Name, "<br/>",
"<b>Concentration: </b>", Concentration, "<br/>",
"<b>Unit: </b>", unit, "<br/>",
"<b>Sample description: </b>", SMC_DESC, "<br/>",
"<b>Date: </b>", Sample_datetime, "<br/>",
"<b>Method: </b>", method, "<br/>",
sep = ""
),
color = "black", # Outline color
fillColor = fillColor, # Fill color
fillOpacity = 0.8, # Opacity of the fill color
weight = 0.5,
group = legend_title
)
}
## TEST:data = data_process_pbms(var_biota = 'Otter')
## leaflet() %>% addTiles() %>% map_fun_pbms(data=data[[1]], var_biota = 'Otter')
## var_map_sgl currently handled by data_fun.R
map_fun_pbms <- function(map, data,
var_biota = "Otter",
# var_map_sgl = "Cd",
fillColor = "blue",
colorPalette = 'Oranges',
legend_title= NULL){
#temporary fix
identical_columns <- sapply(data, function(col) identical(data[['value']], col))# check which one is identical to the column `value`
identical_columns <- identical_columns %>% which() %>% names()
print(identical_columns)
identical_columns <- identical_columns[which(identical_columns !='value')]
var_map_sgl <- identical_columns[1]
print(var_map_sgl)
if(var_biota =='Otter'){
# data <- data %>% mutate(value = !!var_map_sgl)
qpal <- colorBin(colorPalette, data$value, bins = 5, , na.color = 'grey')
map %>%
addCircleMarkers(~long, ~lat, data=data, fillColor = ~qpal(value), group = legend_title,
popup = ~paste(
"<b>UWCRef: </b>", UWCRef, "<br/>",
"<b>Sex: </b>", Sex, "<br/>",
"<b>AgeClass: </b>", AgeClass, "<br/>",
"<b>Year: </b>", year, "<br/>",
"<b>Variable: </b>", var_map_sgl , "<br/>",
"<b>Value: </b>", round(value,digits=2) , "<br/>",
sep = ""
),
color = "black", # Outline color
# fillColor = fillColor, # Fill color
fillOpacity = 0.8, # Opacity of the fill color
weight = 0.5,) %>%
addLegend("bottomright", data=data, pal = qpal, values = ~value,
title = paste(legend_title, "</br>Metals conc. [µg/g dry weight]"),
opacity = 1, group = legend_title
)
} else if(var_biota =='Buzzard'){
# check for no data
if (is.null(data) || nrow(data) == 0 || all(is.na(data$value))) {
# Add a dummy legend
dummy_palette <- colorNumeric(palette = "Greys", domain = c(0, 1)) # Dummy palette
map <- map %>%
addLegend("bottomright", pal = dummy_palette, values = c(0, 1),
title = paste(legend_title, "</br>No data available for this selection"),
opacity = 1)
} else {
# else there is data and continue
# data <- data %>% mutate(value = !!var_map_sgl)
qpal <- colorBin(colorPalette, data$value, bins = 5, , na.color = 'grey')
map = map %>%
addCircleMarkers(~long, ~lat, data=data, fillColor = ~qpal(value),
color = "black", weight = 1.0, group = legend_title,
fillOpacity = 0.8, # Opacity of the fill color
popup = ~paste(
"<b>Sex: </b>", `Sex (Male/Female/Unknown)`, "<br/>",
"<b>AgeClass: </b>", `Age (Adult/Juvenile/Unknown)`, "<br/>",
"<b>Year: </b>", year, "<br/>",
"<b>Variable: </b>", var_map_sgl , "<br/>",
"<b>Value: </b>", value , "<br/>",
sep = ""))
if (var_map_sgl %in% metals_choices){
map = map %>%
addLegend("bottomright", data=data, pal = qpal, values = ~value, group = legend_title,
title = paste(legend_title, "</br>Metals conc. [µg/g dry weight]"),
opacity = 1)
} else if (var_map_sgl %in% SGARs_choices){
map = map %>%
addLegend("bottomright", data=data, pal = qpal, values = ~value, group = legend_title,
title = paste(legend_title, "</br>SGARs conc. [ng/g wet weight]"),
opacity = 1)
} else {
map = map
}
map
}
} else if(var_biota =='Sparrowhawk'){
# data <- data %>% mutate(value = !!var_map_sgl)
qpal2 <- colorBin(colorPalette, data$value, bins = 5, , na.color = 'grey')
map %>%
addCircleMarkers(~long, ~lat, data=data,fillColor = ~qpal2(value),
color = "black", weight = 1.0,
fillOpacity = 0.8, # Opacity of the fill color
group = legend_title,
popup = ~paste(
"<b>AgeClass: </b>", AGE, "<br/>",
"<b>Year: </b>", year, "<br/>",
"<b>Variable: </b>", var_map_sgl , "<br/>",
"<b>Value: </b>", value , "<br/>",
sep = "")) %>%
addLegend("bottomright", data=data, pal = qpal2, values = ~value,
title = paste(legend_title, "</br>SGARs conc. [ng/g wet weight]"),
opacity = 1, group = legend_title)
} else {
map
}
}
## TEST:data = data_process_pfas(var_biota = 'Otter')
## fillColor = colorNumeric(palette = brewer.pal(9, "Reds"), domain = data[[1]]$transform_value)
## leaflet() %>% addTiles() %>% map_fun_pfas(data=data[[1]],fillColor = fillColor)
map_fun_pfas <- function(map, data, fillColor, legend_title = "PFAS", showHeatmap = FALSE){
if (showHeatmap) {
map %>%
addHeatmap(
data = data,
lng = ~Longitude, lat = ~Latitude, intensity = ~transform_value,
blur = 15, radius = 25,
minOpacity = 0.5,
gradient = fillColor, #comment out to use default
group = legend_title
)
} else {
map %>%
# addTiles() %>%
# setView(lng = mean(filtered_data$Longitude), lat = mean(filtered_data$Latitude), zoom = 5) %>%
#addControl(html = paste("<h5>", selected_matrix, " ", selected_substance, " ", start_year, " - ", end_year, "</h5>", sep = ""), position = "topright") %>%
addCircleMarkers(
data = data,
lng = ~Longitude, lat = ~Latitude, radius = 8,
popup = ~paste(
"<b>Matrix: </b>", matrix, "<br/>",
"<b>Substance: </b>", substance, "<br/>",
"<b>Quantity Released: </b>", value, "<br/>",
"<b>Unit: </b>", "ng/l", "<br/>",
#"<b>Quantile Bin (1-3): </b>", substance_value_bin, "<br/>",
"<b>Date: </b>", date, "<br/>",
"<b>Year: </b>", year, "<br/>",
sep = ""
),
color = "black", # Outline color
fillColor = ~fillColor(transform_value), # ~pal(transform_value),
fillOpacity = 0.8, # Opacity of the fill color
weight = 0.2,
group = legend_title
)
}
# %>%
# addLegend("bottomright", pal = pal, values = ~transform_value,
# title = paste(selected_substance, " ng/l"),
# labFormat = labFormat_transform,
# opacity = 1)
}
map_fun_rain <- function(map, data, colors, legend_title = "HadUK-Grid Annual Rainfall") {
#pal <- colorNumeric("viridis", domain = values(data), na.color = "transparent")
map %>%
addRasterImage(data,
colors = colors,
opacity = 0.7,
group = legend_title)
# %>%
# addControl( HTML(paste("<b>Year: </b>", input$year_slider)), position = "topright")
}
## TEST:data = data_process_apiens()[[1]]
## fillColor = colorNumeric(palette = brewer.pal(9, 'Blues'), domain = data$Value)
## leaflet() %>% addTiles() %>% map_fun_apiens(data = data, fillColor=fillColor)
map_fun_apiens <- function(map, data, fillColor= "blue", legend_title = "APIENS"){
map %>%
addCircleMarkers(
data = data,
lng = ~Site_lon, lat = ~Site_lat, radius = 8,
popup = ~paste(
"<b>Site_habitat: </b>", Site_habitat, "<br/>",
"<b>Network: </b>", Network, "<br/>",
"<b>Site_habitat: </b>", Site_habitat, "<br/>",
"<b>Plot_ID_or_Horizon_name: </b>", Plot_ID_or_Horizon_name, "<br/>",
"<b>Year: </b>", Year, "<br/>",
"<b>Variable: </b>", Variable, "<br/>",
"<b>Unit: </b>", Unit, "<br/>",
sep = ""
),
color = "black", # Outline color
fillColor = fillColor, # ~pal(transform_value),
fillOpacity = 0.8, # Opacity of the fill color
weight = 0.2,
group = legend_title
)
}
map_fun_catsdogs <- function(map, map_data, palette_name = 'viridis', legend_title = "Density by postcode") {
pal <- colorNumeric(palette_name, NULL)
head(map_data)
map %>%
addPolygons(data = map_data,
stroke = FALSE, smoothFactor = 0.5, fillOpacity = 0.5, weight = 1, opacity = 1.0,
fillColor = ~pal(Value),
group = legend_title)
}
map_fun_EUSO <- function(map, data, colors, legend_title = "Soil health") {
print('map_process_EUSO')
#pal <- colorNumeric("viridis", domain = values(data), na.color = "transparent")
map %>%
# addRasterImage(data, # can't handle large raster
# colors = colors,
# opacity = 0.7,
# group = legend_title)
leafem::addGeotiff(data,
colorOptions = colorOptions(
palette = hcl.colors(256, palette = "inferno")
, na.color = "transparent"
),
opacity = 0.7,
group = legend_title) %>%
setView(-3.0, 55.5, zoom = 6)
}
map_fun_IYR <- function(map, data, colors, legend_title = "Input to Yield Ratio") {
#pal <- colorNumeric("viridis", domain = values(data), na.color = "transparent")
map %>%
addRasterImage(data,
colors = colors,
opacity = 0.7,
group = legend_title)
}
switch_map <- function(m, map_data, input_choice, legend_title='legend', palette_name = 'Reds', showHeatmap=FALSE){
labFormat_transform = labelFormat(transform = function(x) round(exp(x) - 1, 1))
print(paste0('switch_map', input_choice))
if (input_choice == 'EA water quality GCMS/LCMS data') {
# Check if the dataset is empty or has no valid data
if (nrow(map_data) == 0 || all(is.na(map_data$log_Concentration))) {
dummy_color <- colorNumeric(palette = "Greys", domain = c(0, 1))
# Add a message in the legend indicating no data
m = m %>% addLegend(
position = "bottomright",
pal = dummy_color,
values = c(0, 1),
title = paste0(legend_title, "</br>", "No data available for this selection"),
opacity = 1
)
} else {
fillColor = colorNumeric(palette = brewer.pal(9,palette_name), domain = map_data$log_Concentration)
m = m %>% map_fun_EA_WQ_gcms(map_data,
fillColor = ~fillColor(log_Concentration),
legend_title= legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = ~map_data$log_Concentration,
title = paste0(legend_title ,"</br>","Concentration ug/l"),
opacity = 1,
group = legend_title,
labFormat = labFormat_transform)
}
} else if (input_choice == 'EA pollution inventory 2021') {
#m = m %>% map_fun_EA_pollution(map_data,fillColor = color_data$RGB[new_id_ii])
fillColor = colorNumeric(palette = brewer.pal(9,palette_name), domain = map_data$log_quantity_released_tons)
m = m %>% map_fun_EA_pollution(map_data,
fillColor = ~fillColor(log_quantity_released_tons),
legend_title= legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = map_data$log_quantity_released_tons,
title = paste0(legend_title ,"</br>","tonnes"),
opacity = 1,
group = legend_title,
labFormat = labFormat_transform)
} else if (input_choice == 'Predatory Bird Monitoring Scheme') {
# added a trycatch for when there is no data for the selection
m <- tryCatch({m %>% map_fun_pbms(map_data,
colorPalette =palette_name,
var_biota = map_data$biota[1],
legend_title= legend_title)
}, error = function(e){
dummy_palette <- colorNumeric(palette = "Greys", domain = c(0, 0)) # Dummy palette
# add notification
showNotification("No data available for this selection.", type = "error", duration = 5)
# Add dummy legend with message
m %>% addLegend("bottomright", pal = dummy_palette, values = c(0, 0),
title = paste(legend_title, "</br>No data available for this selection"),
opacity = 1)
})
} else if (input_choice == 'PFAS') {
# Check if the dataset is empty or has no valid data
if (nrow(map_data) == 0 || all(is.na(map_data$transform_value))) {
dummy_palette <- colorNumeric(palette = "Greys", domain = c(0, 0)) # Dummy palette
showNotification("No data available for this selection.", type = "error", duration = 5)
# Add a message in the legend indicating no data
m = m %>% addLegend(
position = "bottomright",
pal = dummy_palette,
values = c(0, 0),
title = paste0(legend_title, "</br>", "No data available for this selection"),
opacity = 1
)
} else {
#m = m %>% map_fun_pfas(map_data,fillColor = color_data$RGB[new_id_ii])
# labFormat_transform = labelFormat(transform = function(x) round(exp(x) - 1, 1))
selected_palette <-palette_name
fillColor = colorNumeric(palette = brewer.pal(9, selected_palette), domain = map_data$transform_value)
gradient_colors <- colorNumeric(
palette = brewer.pal(9, selected_palette),
domain = map_data$transform_value
)(seq(min(map_data$transform_value, na.rm = TRUE),
max(map_data$transform_value, na.rm = TRUE),
length.out = 256))
m = m %>% map_fun_pfas(map_data,
fillColor = if (showHeatmap) gradient_colors else fillColor, # Use gradient_colors in heatmap mode
legend_title= legend_title,
showHeatmap = showHeatmap
) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = map_data$transform_value,
title = paste0(legend_title ,"</br>","ng/l"),
opacity = 1,
group = legend_title,
labFormat = labFormat_transform)
}
} else if (input_choice == "HadUK-Grid Annual Rainfall") {
rain_values <- values(map_data)
rain_values <- rain_values[!is.na(rain_values)]
fillColor <- colorNumeric(
palette = brewer.pal(9,palette_name),
domain=range(rain_values),
na.color = "transparent"
)
m = m %>% map_fun_rain(map_data,
colors = fillColor,
legend_title = legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = values(map_data),
title = paste0(legend_title ,"</br>","mm"),
group = legend_title,
na.label = NULL)
} else if (input_choice == 'APIENS') {
#m = m %>% map_fun_EA_pollution(map_data,fillColor = color_data$RGB[new_id_ii])
fillColor = colorNumeric(palette = brewer.pal(9,palette_name), domain = map_data$Value)
m = m %>% map_fun_apiens(map_data,
fillColor = ~fillColor(Value),
legend_title= legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = ~map_data$Value,
title = paste0(legend_title ,"</br>",unique(map_data$Unit)),
opacity = 1,
group = legend_title)
} else if (input_choice == 'UK cats and dogs density') {
m = m %>% map_fun_catsdogs(map_data,
palette_name = palette_name,
legend_title= legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = colorNumeric(palette_name, NULL),
values = ~Value,
title = paste0(legend_title),
opacity = 1,
group = legend_title)
} else if (input_choice == "HadUK-Grid Annual Rainfall") {
rain_values <- values(map_data)
rain_values <- rain_values[!is.na(rain_values)]
fillColor <- colorNumeric(
palette = brewer.pal(9,palette_name),
domain=range(rain_values),
na.color = "transparent"
)
m = m %>% map_fun_rain(map_data,
colors = fillColor,
legend_title = legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = values(map_data),
title = paste0(legend_title ,"</br>","mm"),
group = legend_title,
na.label = NULL)
} else if (input_choice == "EU Soil metals") {
#EUSO_values <- values(map_data)
# EUSO_values <- EUSO_values[!is.na(EUSO_values)]
# fillColor <- colorNumeric(
# palette = brewer.pal(9,palette_name),
# domain=range(EUSO_values),
# na.color = "transparent"
# )
m = m %>% map_fun_EUSO(map_data,
colors = fillColor,
legend_title = legend_title) #%>%
# addLegend(data = map_data,
# position = "bottomright",
# pal = fillColor,
# values = values(map_data),
# title = paste0(legend_title ,"</br>","[mg Kg-1]"),
# group = legend_title,
# na.label = NULL)
} else if (input_choice == "AgZero+ Input to Yield Ratio (IYR)") {
IYR_values <- values(map_data)
IYR_values <- IYR_values[!is.na(IYR_values)]
fillColor <- colorNumeric(
palette = brewer.pal(9,palette_name),
domain=range(IYR_values),
na.color = "transparent"
)
m = m %>% map_fun_IYR(map_data,
colors = fillColor,
legend_title = legend_title) %>%
addLegend(data = map_data,
position = "bottomright",
pal = fillColor,
values = values(map_data),
title = paste0(legend_title ,"</br>","[unitless]"),
group = legend_title,
na.label = NULL)
}
return(m)
}