I am trying to put on a Italian geographical map a dot reporting the provenience ('provincia') of our patients. Ideally, the dot size should be proportional to the number of patients coming from that 'provincia'. An example of the list I would like to plot is the following.
MI 8319
CO 537
MB 436
VA 338
BG 310
PV 254
CR 244
NO 210
RM 189
CS 179
In the first column there is the 'provincia' code: MI (Milano), CO (Como), MB (Monza-Brianza), etc. In the second column there is the number of patients from that 'provincia'. So the output should be an Italian political map where the biggest dot is around the city of Milano (MI), the second biggest dot is near the city of Como (CO), the third one is around the city of Monza-Brianza (MB),etc.
Is there any package that could do the plot I am looking for? I found a tool that could do the job here, but apparently they expect that I load the geographical coordinates in order to do the plot.
https://www.littlemissdata.com/blog/maps
Thanks in advance.
Here is one way to handle your task. You have the abbreviations for Italian province. You want to use them to merge your data with polygon data. If you download Italy's polygons from GADM, you can obtain data that contain the abbreviations. Specifically, the column, HASC_2 is the one. You need to merge your data with the polygon data. Then, you want to create another data set which contains centroid. You can draw a map with the two data sets.
library(tidyverse)
library(sf)
library(ggthemes)
# Get the sf file from https://gadm.org/download_country_v3.html
# and import it in R.
mysf <- readRDS("gadm36_ITA_2_sf.rds")
# This is your data, which is called mydata.
mydata <- structure(list(abbs = c("MI", "CO", "MB", "VA", "BG", "PV", "CR",
"NO", "RM", "CS"), value = c(8319L, 537L, 436L, 338L, 310L, 254L,
244L, 210L, 189L, 179L)), class = "data.frame", row.names = c(NA,
-10L))
abbs value
1 MI 8319
2 CO 537
3 MB 436
4 VA 338
5 BG 310
6 PV 254
7 CR 244
8 NO 210
9 RM 189
10 CS 179
# Abbreviations are in HASC_2 in mysf. Manipulate strings so that
# I can join mydata with mysf with the abbreviations. I also get
# longitude and latitude with st_centroid(). This data set is for
# geom_point().
mysf2 <- mutate(mysf, HASC_2 = sub(x = HASC_2, pattern = "^IT.", replacement = "")) %>%
left_join(mydata, by = c("HASC_2" = "abbs")) %>%
mutate(lon = map_dbl(geometry, ~st_centroid(.x)[[1]]),
lat = map_dbl(geometry, ~st_centroid(.x)[[2]]))
# Draw a map
ggplot() +
geom_sf(data = mysf) +
geom_point(data = mysf2, aes(x = lon, y = lat, size = value)) +
theme_map()
UPDATE ON INSET MAP
This is an update following different suggestion on using inset maps, which I think it would be the best solution for yout question and comments:
library(sf)
library(cartography)
EU = st_read("~/R/mapslib/EUROSTAT/NUTS_RG_03M_2016_3035_LEVL_3.geojson")
IT = subset(EU, CNTR_CODE == "IT")
mydata <-
structure(list(
abbs = c("MI", "CO", "MB", "VA", "BG", "PV", "CR",
"NO", "RM", "CS"),
value = c(8319L, 537L, 436L, 338L, 310L, 254L,
244L, 210L, 189L, 179L),
nuts = c("ITC4C","ITC42","ITC4D","ITC41",
"ITC46", "ITC48","ITC4A","ITC15",
"ITI43","ITF61")
),
class = "data.frame",
row.names = c(NA, -10L))
patients = merge(IT, mydata, by.x = "id", by.y = "nuts")
#Get breaks for map
br=getBreaks(patients$value)
#Delimit zone
#Based on NUTS1, Nortwest Italy
par(mar=c(0,0,0,0))
ghostLayer(IT[grep("ITC",IT$NUTS_ID),], bg="lightblue")
plot(st_geometry(EU), col="grey90", add=TRUE)
plot(st_geometry(IT), col = "#FEFEE9", border = "#646464", add=TRUE)
choroLayer(
patients,
var = "value",
breaks = br,
col = carto.pal(pal1 = "red.pal", n1 = length(br)-1),
legend.pos = "topleft",
legend.title.txt = "Total patients",
add = TRUE,
legend.frame = TRUE
)
labelLayer(patients,txt="abbs", halo=TRUE, overlap = FALSE)
#Inset
par(
fig = c(0, 0.4, 0.01, 0.4),
new = TRUE
)
inset=patients[patients$abbs %in% c("RM","CS"),]
ghostLayer(inset, bg="lightblue")
plot(st_geometry(EU), col="grey90", add=TRUE)
plot(st_geometry(IT), col = "#FEFEE9", border = "#646464", add=TRUE)
choroLayer(
patients,
var = "value",
breaks = br,
col = carto.pal(pal1 = "red.pal", n1 = length(br)-1),
legend.pos = "n",
add = TRUE
)
labelLayer(patients,txt="abbs", halo=TRUE, overlap = FALSE)
box(which = "figure", lwd = 1)
#RESTORE PLOT
par(fig=c(0,1,0,1))
OLD ANSWER
Following my comment on plotting labels, maybe with circles is not the best option for your map, given the concentration. I suggest you to use another kind of map for that, as chorolayer, I leveraged on https://stackoverflow.com/users/3304471/jazzurro for the dataframe.
library(sf)
library(cartography)
EU = st_read("~/R/mapslib/EUROSTAT/NUTS_RG_03M_2016_3035_LEVL_3.geojson")
IT = subset(EU, CNTR_CODE == "IT")
mydata <-
structure(list(
abbs = c("MI", "CO", "MB", "VA", "BG", "PV", "CR",
"NO", "RM", "CS"),
value = c(8319L, 537L, 436L, 338L, 310L, 254L,
244L, 210L, 189L, 179L),
nuts = c("ITC4C","ITC42","ITC4D","ITC41",
"ITC46", "ITC48","ITC4A","ITC15",
"ITI43","ITF61")
),
class = "data.frame",
row.names = c(NA, -10L))
patients = merge(IT, mydata, by.x = "id", by.y = "nuts")
#Options1 - With circles
par(mar = c(0, 0, 0, 0))
plot(st_geometry(IT), col = "#FEFEE9", border = "#646464")
propSymbolsLayer(
x = patients,
var = "value",
col = carto.pal(pal1 = "red.pal", n1 = 6),
legend.title.txt = "Total patients",
add = TRUE
)
#Option 2 - Chorolayer with labels
par(mar = c(0, 0, 0, 0))
plot(st_geometry(IT), col = "#FEFEE9", border = "#646464")
choroLayer(
patients,
var = "value",
col = carto.pal(pal1 = "red.pal", n1 = 6),
legend.title.txt = "Total patients",
add = TRUE
)
#Create labels
patients$label = paste(patients$abbs, patients$value, sep = " - ")
labelLayer(
patients,
txt = "label",
overlap = FALSE,
halo = TRUE,
show.lines = TRUE,
)
Data from
https://ec.europa.eu/eurostat/cache/GISCO/distribution/v2/nuts/nuts-2016-files.html
I am trying to plot flow map (for singapore) . I have Entry(Lat,Long) and Exit (Lat,long). I am trying to map the flow from entry to exit in singapore map.
structure(list(token_id = c(1.12374e+19, 1.12374e+19, 1.81313e+19,
1.85075e+19, 1.30752e+19, 1.30752e+19, 1.32828e+19, 1.70088e+19,
1.70088e+19, 1.70088e+19, 1.05536e+19, 1.44818e+19, 1.44736e+19,
1.44736e+19, 1.44736e+19, 1.44736e+19, 1.89909e+19, 1.15795e+19,
1.15795e+19, 1.15795e+19, 1.70234e+19, 1.70234e+19, 1.44062e+19,
1.21512e+19, 1.21512e+19, 1.95909e+19, 1.95909e+19, 1.50179e+19,
1.50179e+19, 1.24174e+19, 1.36445e+19, 1.98549e+19, 1.92068e+19,
1.18468e+19, 1.18468e+19, 1.92409e+19, 1.92409e+19, 1.21387e+19,
1.9162e+19, 1.9162e+19, 1.40385e+19, 1.40385e+19, 1.32996e+19,
1.32996e+19, 1.69103e+19, 1.69103e+19, 1.57387e+19, 1.40552e+19,
1.40552e+19, 1.00302e+19), Entry_Station_Lat = c(1.31509, 1.33261,
1.28425, 1.31812, 1.33858, 1.29287, 1.39692, 1.37773, 1.33858,
1.33322, 1.28179, 1.30036, 1.43697, 1.39752, 1.27637, 1.39752,
1.41747, 1.35733, 1.28405, 1.37773, 1.35898, 1.42948, 1.32774,
1.42948, 1.349, 1.36017, 1.34971, 1.38451, 1.31509, 1.31509,
1.37002, 1.34971, 1.31231, 1.39169, 1.31812, 1.44909, 1.29341,
1.41747, 1.33759, 1.44062, 1.31509, 1.38451, 1.29461, 1.32388,
1.41747, 1.27614, 1.39752, 1.39449, 1.33261, 1.31231), Entry_Station_Long = c(103.76525,
103.84718, 103.84329, 103.89308, 103.70611, 103.8526, 103.90902,
103.76339, 103.70611, 103.74217, 103.859, 103.85563, 103.7865,
103.74745, 103.84596, 103.74745, 103.83298, 103.9884, 103.85152,
103.76339, 103.75191, 103.83505, 103.67828, 103.83505, 103.74956,
103.88504, 103.87326, 103.74437, 103.76525, 103.76525, 103.84955,
103.87326, 103.83793, 103.89548, 103.89308, 103.82004, 103.78479,
103.83298, 103.69742, 103.80098, 103.76525, 103.74437, 103.80605,
103.93002, 103.83298, 103.79156, 103.74745, 103.90051, 103.84718,
103.83793), Exit_Station_Lat = structure(c(48L, 34L, 118L, 60L,
14L, 54L, 10L, 49L, 49L, 74L, 71L, 65L, 102L, 5L, 102L, 119L,
116L, 10L, 13L, 88L, 117L, 66L, 40L, 62L, 117L, 37L, 67L, 34L,
85L, 44L, 102L, 44L, 115L, 29L, 92L, 17L, 121L, 70L, 120L, 52L,
85L, 34L, 42L, 11L, 4L, 115L, 62L, 48L, 92L, 14L), .Label = c("1.27082",
"1.27091", "1.27236", "1.27614", "1.27637", "1.27646", "1.27935",
"1.28221", "1.28247", "1.28405", "1.28621", "1.28819", "1.28932",
"1.29287", "1.29309", "1.29338", "1.29341", "1.29461", "1.29694",
"1.29959", "1.29974", "1.30034", "1.30252", "1.30287", "1.30392",
"1.30394", "1.30619", "1.30736", "1.30842", "1.31139", "1.3115",
"1.31167", "1.31188", "1.31509", "1.31654", "1.31756", "1.31913",
"1.31977", "1.32008", "1.3205", "1.32104", "1.32388", "1.32573",
"1.32725", "1.32774", "1.33119", "1.33155", "1.33261", "1.33322",
"1.33474", "1.33554", "1.33759", "1.33764", "1.33858", "1.33921",
"1.34037", "1.34225", "1.34293", "1.3432", "1.34426", "1.34857",
"1.349", "1.34905", "1.35158", "1.35733", "1.35898", "1.36017",
"1.3625", "1.36849", "1.37002", "1.37121", "1.37304", "1.37666",
"1.37775", "1.3786", "1.37862", "1.38001", "1.38029", "1.3803",
"1.38178", "1.38269", "1.38295", "1.38399", "1.38423", "1.38451",
"1.38671", "1.38672", "1.38777", "1.38814", "1.3894", "1.39147",
"1.39169", "1.39189", "1.39208", "1.39389", "1.39449", "1.39452",
"1.39628", "1.39692", "1.39717", "1.39732", "1.39752", "1.39821",
"1.39928", "1.39962", "1.4023", "1.40455", "1.40511", "1.40524",
"1.40843", "1.40961", "1.41184", "1.41588", "1.41685", "1.41747",
"1.42526", "1.42948", "1.43256", "1.43697", "1.44062", "1.44909"
), class = "factor"), Exit_Station_Long = structure(c(59L, 19L,
27L, 4L, 65L, 3L, 63L, 6L, 6L, 21L, 93L, 121L, 9L, 56L, 9L, 32L,
16L, 63L, 44L, 23L, 50L, 12L, 54L, 11L, 50L, 71L, 87L, 19L, 7L,
118L, 9L, 118L, 49L, 90L, 96L, 31L, 45L, 61L, 38L, 2L, 7L, 19L,
117L, 47L, 34L, 49L, 11L, 59L, 96L, 65L), .Label = c("103.67828",
"103.69742", "103.70611", "103.72092", "103.73274", "103.74217",
"103.74437", "103.74529", "103.74745", "103.74905", "103.74956",
"103.75191", "103.7537", "103.75803", "103.76011", "103.76215",
"103.76237", "103.76449", "103.76525", "103.76648", "103.76667",
"103.76893", "103.7696", "103.77082", "103.77145", "103.77266",
"103.774", "103.77866", "103.78185", "103.78425", "103.78479",
"103.7865", "103.78744", "103.79156", "103.79631", "103.79654",
"103.79836", "103.80098", "103.803", "103.80605", "103.80745",
"103.80781", "103.80978", "103.81703", "103.82004", "103.82592",
"103.82695", "103.83216", "103.83298", "103.83505", "103.83918",
"103.83953", "103.83974", "103.84387", "103.84496", "103.84596",
"103.84673", "103.84674", "103.84718", "103.84823", "103.84955",
"103.85092", "103.85152", "103.85226", "103.8526", "103.85267",
"103.85436", "103.85446", "103.85452", "103.86088", "103.86149",
"103.86275", "103.86291", "103.86395", "103.86405", "103.86896",
"103.87087", "103.87135", "103.87534", "103.87563", "103.8763",
"103.87971", "103.88003", "103.88126", "103.88243", "103.88296",
"103.88504", "103.8858", "103.88816", "103.8886", "103.88934",
"103.89054", "103.89237", "103.89313", "103.8938", "103.89548",
"103.89719", "103.89723", "103.89854", "103.9003", "103.90051",
"103.90208", "103.90214", "103.9031", "103.90484", "103.90537",
"103.90597", "103.90599", "103.90663", "103.9086", "103.90902",
"103.9126", "103.9127", "103.91296", "103.91616", "103.9165",
"103.93002", "103.94638", "103.94929", "103.95337", "103.9884"
), class = "factor")), .Names = c("token_id", "Entry_Station_Lat",
"Entry_Station_Long", "Exit_Station_Lat", "Exit_Station_Long"
), row.names = c(10807L, 10808L, 10810L, 10815L, 10817L, 10818L,
10819L, 10820L, 10823L, 10824L, 10826L, 10827L, 10829L, 10831L,
10832L, 10833L, 10834L, 10835L, 10836L, 10838L, 10840L, 10841L,
10843L, 10847L, 10850L, 10852L, 10854L, 10855L, 10859L, 10861L,
10869L, 10872L, 10883L, 10886L, 10891L, 10895L, 10896L, 10897L,
10900L, 10902L, 10903L, 10906L, 10910L, 10911L, 10912L, 10913L,
10915L, 10920L, 10921L, 10924L), class = "data.frame")
I am trying to get something this : Map Flow
Just realized that the original solution usin geom_path was more complicated than necessary. geom_segmentworks without changing the data:
require(ggplot2)
require(ggmap)
basemap <- get_map("Singapore",
source = "stamen",
maptype = "toner",
zoom = 11)
g = ggplot(a)
map = ggmap(basemap, base_layer = g)
map = map + coord_cartesian() +
geom_curve(size = 1.3,
aes(x=as.numeric(Entry_Station_Long),
y=as.numeric(Entry_Station_Lat),
xend=as.numeric(as.character(Exit_Station_Long)),
yend=as.numeric(as.character(Exit_Station_Lat)),
color=as.factor(token_id)))
map
This solution leverages Draw curved lines in ggmap, geom_curve not working to implement curved lines on a map.
ggmaps used for simplicity - for more ambitious projects I would recommend leaflet.
Below the solution using a long data format with some prior data wrangling. It also uses straight lines instead of the curves above.
a %>%
mutate(path = row_number()) -> a
origin = select(a,token_id,Entry_Station_Lat,Entry_Station_Long,path)
origin$type = "origin"
dest = select(a,token_id,Exit_Station_Lat,Exit_Station_Long,path)
dest$type = "dest"
colnames(origin) = c("id","lat","long","path","type")
colnames(dest) = c("id","lat","long","path","type")
complete = rbind(origin,dest)
complete %>% arrange(path,type) -> complete
require(ggmap)
basemap <- get_map("Singapore",
source = "stamen",
maptype = "toner",
zoom = 11)
g = ggplot(complete, aes(x=as.numeric(long),
y=as.numeric(lat)))
map = ggmap(basemap, base_layer = g)
map + geom_path(aes(color = as.factor(id)),
size = 1.1)
If you want to plot it on an actual Google Map, and recreate the style of your linked map, you can use my googleway package that uses Google's Maps API. You need an API key to use their maps
library(googleway)
df$Exit_Station_Lat <- as.numeric(as.character(df$Exit_Station_Lat))
df$Exit_Station_Long <- as.numeric(as.character(df$Exit_Station_Long))
df$polyline <- apply(df, 1, function(x) {
lat <- c(x['Entry_Station_Lat'], x['Exit_Station_Lat'])
lon <- c(x['Entry_Station_Long'], x['Exit_Station_Long'])
encode_pl(lat = lat, lon = lon)
})
mapKey <- 'your_api_key'
style <- '[ { "stylers": [{ "visibility": "simplified"}]},{"stylers": [{"color": "#131314"}]},{"featureType": "water","stylers": [{"color": "#131313"},{"lightness": 7}]},{"elementType": "labels.text.fill","stylers": [{"visibility": "on"},{"lightness": 25}]}]'
google_map(key = mapKey, style = style) %>%
add_polylines(data = df,
polyline = "polyline",
mouse_over_group = "Entry_Station_Lat",
stroke_weight = 0.7,
stroke_opacity = 0.5,
stroke_colour = "#ccffff")
Note, to recreate the map using flight data, see the example given in ?add_polylines
You can also show other types of routes, for example, driving between the locations by using Google's Directions API to encode the driving routes.
df$drivingRoute <- lst_directions <- apply(df, 1, function(x){
orig <- as.numeric(c(x['Entry_Station_Lat'], x['Entry_Station_Long']))
dest <- as.numeric(c(x['Exit_Station_Lat'], x['Exit_Station_Long']))
dir <- google_directions(origin = orig, destination = dest, key = apiKey)
dir$routes$overview_polyline$points
})
google_map(key = mapKey, style = style) %>%
add_polylines(data = df,
polyline = "drivingRoute",
mouse_over_group = "Entry_Station_Lat",
stroke_weight = 0.7,
stroke_opacity = 0.5,
stroke_colour = "#ccffff")
Alternative answer using leaflet and geosphere
#get Packages
require(leaflet)
require(geosphere)
#format data
a$Entry_Station_Long = as.numeric(as.character(a$Entry_Station_Long))
a$Entry_Station_Lat = as.numeric(as.character(a$Entry_Station_Lat))
a$Exit_Station_Long = as.numeric(as.character(a$Exit_Station_Long))
a$Exit_Station_Lat = as.numeric(as.character(a$Exit_Station_Lat))
a$id = as.factor(as.numeric(as.factor(a$token_id)))
#create some colors
factpal <- colorFactor(heat.colors(30), pathList$id)
#create a list of interpolated paths
pathList = NULL
for(i in 1:nrow(a))
{
tmp = gcIntermediate(c(a$Entry_Station_Long[i],
a$Entry_Station_Lat[i]),
c(a$Exit_Station_Long[i],
a$Exit_Station_Lat[i]),n = 25,
addStartEnd=TRUE)
tmp = data.frame(tmp)
tmp$id = a[i,]$id
tmp$color = factpal(a[i,]$id)
pathList = c(pathList,list(tmp))
}
#create empty base leaflet object
leaflet() %>% addTiles() -> lf
#add each entry of pathlist to the leaflet object
for (path in pathList)
{
lf %>% addPolylines(data = path,
lng = ~lon,
lat = ~lat,
color = ~color) -> lf
}
#show output
lf
Note that as I mentioned before there is no way of geosphering the paths in such a small locality - the great circles are effectively straight lines. If you want the rounded edges for sake of aesthetics you may have to use the geom_curve way described in my other answer.
I've also written the mapdeck library to make visualisations like this more appealing*
library(mapdeck)
set_token("MAPBOX_TOKEN") ## set your mapbox token here
df$Exit_Station_Lat <- as.numeric(as.character(df$Exit_Station_Lat))
df$Exit_Station_Long <- as.numeric(as.character(df$Exit_Station_Long))
mapdeck(
style = mapdeck_style('dark')
, location = c(104, 1)
, zoom = 8
, pitch = 45
) %>%
add_arc(
data = df
, origin = c("Entry_Station_Long", "Entry_Station_Lat")
, destination = c("Exit_Station_Long", "Exit_Station_Lat")
, layer_id = 'arcs'
, stroke_from_opacity = 100
, stroke_to_opacity = 100
, stroke_width = 3
, stroke_from = "#ccffff"
, stroke_to = "#ccffff"
)
*subjectively speaking
I would like to leave an alternative approach for you. What you can do is to restructure your data. Right now you have two columns for entry stations and the other two for exit stations. You can create one column for long, and another for lat by combing these columns. The trick is to use rbind() and c().
Let's have a look of this simple example.
x <- c(1, 3, 5)
y <- c(2, 4, 6)
c(rbind(x, y))
#[1] 1 2 3 4 5 6
Imagine x is long for entry stations and y for exit stations. 1 is longitude for a starting point. 2 is longitude where the first journey ended. As far as I can see from your sample data, it seems that 3 is identical 2. You could remove duplicated data points for each token_id. If you have a large set of data, perhaps this is something you want to consider. Back to the main point, you can create a column with longitude in the sequence you want with the combination of the two functions. Since you said you have date information, make sure you order the data by date. Then, the sequence of each journey appears in the right way in tmp. You want to do this with latitude as well.
Now we look into your sample data. It seems that Exit_Station_Lat and Exit_Station_Long are in factor. The first operation is to convert them to numeric. Then, you apply the method above and create a data frame. I called your data mydf.
library(dplyr)
library(ggplot2)
library(ggalt)
library(ggthemes)
library(raster)
mydf %>%
mutate_at(vars(Exit_Station_Lat: Exit_Station_Long),
funs(as.numeric(as.character(.)))) -> mydf
group_by(mydf, token_id) %>%
do(data.frame(long = c(rbind(.$Entry_Station_Long,.$Exit_Station_Long)),
lat = c(rbind(.$Entry_Station_Lat, .$Exit_Station_Lat))
)
) -> tmp
Now let's get a map data from GADM. You can download data using the raster package.
getData(name = "GADM", country = "singapore", level = 0) %>%
fortify -> singapore
Finally, you draw a map. The key thing is to use group in aes in geom_path(). I hope this will let you move forward.
ggplot() +
geom_cartogram(data = singapore,
aes(x = long, y = lat, map_id = id),
map = singapore) +
geom_path(data = tmp,
aes(x = long, y = lat, group = token_id,
color = as.character(token_id)),
show.legend = FALSE) +
theme_map()