Making Static & Interactive Maps With ggvis (+ using ggvis maps w/shiny)

December 29, 2014
By

(This article was first published on rud.is » R, and kindly contributed to R-bloggers)

Even though it’s still at version 0.4, the ggvis package has quite a bit of functionality and is highly useful for exploratory data analysis (EDA). I wanted to see how geographical visualizations would work under it, so I put together six examples that show how to use various features of ggvis for presenting static & interactive cartographic creations. Specifically, the combined exercises demonstrate:

  • basic map creation
  • basic maps with points/labels
  • dynamic choropleths (with various scales & tooltips)
  • applying projections and custom color fills (w/tooltips)
  • apply projections and projecting coordinates for plotting (w/tooltips that handle missing data well)

If you want to skip the post and head straight to the code you can head on over to github, peruse the R markdown file on RPubs or play with the shiny version. You’ll need that code to actually run any of the snippets below since I’m leaving out some code-cruft for brevity. Also, all the map graphics below were generated by saving the ggvis output as PNG files (for best browser compatibility), right from the ggvis renderer popup. Click/tap each for a larger version.

Basic Polygons

1

Even though we still need the help of ggplot2‘s fortify, it’s pretty straightforward to crank out a basic map in ggvis:

maine <- readOGR("data/maine.geojson", "OGRGeoJSON")
 
map <- ggplot2::fortify(maine, region="name")
 
map %>%
  ggvis(~long, ~lat) %>%
  group_by(group, id) %>%
  layer_paths(strokeOpacity:=0.5, stroke:="#7f7f7f") %>%
  hide_legend("fill") %>%
  hide_axis("x") %>% hide_axis("y") %>%
  set_options(width=400, height=600, keep_aspect=TRUE)

The code is very similar to one of the ways we render the same image in ggplot. We first read in the shapefile, convert it into a data frame we can use for plotting, group the polygons properly, render them with layer_paths and get rid of chart junk. Now, ggvis (to my knowledge as of this post) has no equivalent of coord_map, so we have to rely on the positioning in the projection and work out the proper height and width parameters to use with a uniform aspect ratio (keep_aspect=TRUE).

For those not familiar with ggvis the ~ operator lets us tell ggivs which columns (or expressions using columns) to map to function parameters and := operator just tells it to use a raw, un-scaled value. You can find out more about why the tilde was chosen or about the various other special operators.

Basic Annotations

2

You can annotate maps in an equally straightforward way.

county_centers <- maine %>%
  gCentroid(byid=TRUE) %>%
  data.frame %>%
  cbind(name=maine$name %>% gsub(" County, ME", "", .) )
 
map %>%
  group_by(group, id) %>%
  ggvis(~long, ~lat) %>%
  layer_paths(strokeWidth:=0.25, stroke:="#7f7f7f") %>%
  layer_points(data=county_centers, x=~x, y=~y, size:=8) %>%
  layer_text(data=county_centers,
             x=~x+0.05, y=~y, text:=~name,
             baseline:="middle", fontSize:=8) %>%
  hide_legend("fill") %>%
  hide_axis("x") %>% hide_axis("y") %>%
  set_options(width=400, height=600, keep_aspect=TRUE)

Note that the group_by works both before or after the ggvis call. Consistent pipe idioms FTW!

Here, we’re making a data frame out of the county centroids and names then using that in a call to layer_points and layer_text. Note how you can change the data source for each layer (just like in ggplot) and use expressions just like in ggplot (we moved the text just slightly to the right of the dot).

Since ggvis outputs vega and uses D3 for rendering, you should probably take a peek at those frameworks as it will help you understand the parameter name differences between ggvis and ggplot.

Basic Choropleths

3

There are actually two examples of this basic state choropleth in the code, but one just uses a different color scale, so I’ll just post the code for one here. This is also designed for interactivity (it has tooltips and lets you change the fill variable) so you should run it locally or look at the shiny version.

"))}   map %>% group_by(group, id)%>% ggvis(~long, ~lat)%>% layer_paths(fill=input_select(label="Crime:", choices=crime_1k %>% select(ends_with("1k"))%>%colnames%>%sort, id="Crime", map=as.name), strokeWidth:=0.5, stroke:="white")%>% scale_numeric("fill", range=c("#bfd3e6", "#8c6bb1" ,"#4d004b"))%>% add_tooltip(crime_values, "hover")%>% add_legend("fill", title="Crime Rate/1K Pop")%>% hide_axis("x")%>% hide_axis("y")%>% set_options(width=400, height=600, keep_aspect=TRUE)
# read in some crime & population data for maine counties
me_pop <- read.csv("data/me_pop.csv", stringsAsFactors=FALSE)
me_crime <- read.csv("data/me_crime.csv", stringsAsFactors=FALSE)
 
# get it into a form we can use (and only use 2013 data)
 
crime_1k <- me_crime %>%
  filter(year==2013) %>%
  select(1,5:12) %>%
  left_join(me_pop) %>%
  mutate(murder_1k=1000*(murder/population_2010),
         rape_1k=1000*(rape/population_2010),
         robbery_1k=1000*(robbery/population_2010),
         aggravated_assault_1k=1000*(aggravated_assault/population_2010),
         burglary_1k=1000*(burglary/population_2010),
         larceny_1k=1000*(larceny/population_2010),
         motor_vehicle_theft_1k=1000*(motor_vehicle_theft/population_2010),
         arson_1k=1000*(arson/population_2010))
 
# normalize the county names
 
map %<>% mutate(id=gsub(" County, ME", "", id)) %>%
  left_join(crime_1k, by=c("id"="county"))
 
# this is for the tooltip. it does a lookup into the crime data frame and
# then uses those values for the popup
 
crime_values <- function(x) {
  if(is.null(x)) return(NULL)
  y <- me_crime %>% filter(year==2013, county==x$id) %>% select(1,5:12)
  sprintf("%s
"
, paste0("
", names(y), ":", format(y), collapse="

You can omit the input_select bit if you just want to do a single choropleth (just map fill to a single variable). The input_select tells ggvis to make a minimal bootstrap sidebar-layout scaffold around the actual graphic to enable variable interaction. In this case we let the user explore different types of crimes (by 1K population) and we also have a tooltip that shows the #’s of each crime in each county as we hover.

Projections and Custom Colors

4

We’re pretty much (mostly) re-creating a previous post in this example and making a projected U.S. map with drought data (as of 2014-12-23).

"))}   map_d %>% group_by(group, id)%>% ggvis(~long, ~lat)%>% layer_paths(fill:=~fill_col, strokeOpacity :=0.5, strokeWidth :=0.25)%>% add_tooltip(drought_values, "hover")%>% hide_legend("fill")%>% hide_axis("x")%>% hide_axis("y")%>% set_options(width=900, height=600, keep_aspect=TRUE)
us <- readOGR("data/us.geojson", "OGRGeoJSON")
us <- us[!us$STATEFP %in% c("02", "15", "72"),]
 
# same method to change the projection
 
us_aea <- spTransform(us, CRS("+proj=laea +lat_0=45 +lon_0=-100 +x_0=0 +y_0=0 +a=6370997 +b=6370997 +units=m +no_defs"))
 
map <- ggplot2::fortify(us_aea, region="GEOID")
 
droughts <- read.csv("data/dm_export_county_20141223.csv")
droughts$id <- sprintf("%05d", as.numeric(as.character(droughts$FIPS)))
droughts$total <- with(droughts, (D0+D1+D2+D3+D4)/5)
 
map_d <- merge(map, droughts, all.x=TRUE)
 
# pre-make custom colors per county
 
ramp <- colorRampPalette(c("white", brewer.pal(n=9, name="YlOrRd")), space="Lab")
 
map_d$fill_col <- as.character(cut(map_d$total, seq(0,100,10), include.lowest=TRUE, labels=ramp(10)))
map_d$fill_col <- ifelse(is.na(map_d$fill_col), "#FFFFFF", map_d$fill_col)
 
drought_values <- function(x) {
  if(is.null(x) | !(x$id %in% droughts$id)) return(NULL)
  y <- droughts %>% filter(id==x$id) %>% select(1,3,4,6:10)
  sprintf("%s
"
, paste0("
", names(y), ":", format(y), collapse="

It’s really similar to the previous code (and you may/should be familiar with the Albers transform from the previous post).

World Domination

5

world <- readOGR("data/ne_50m_admin_0_countries.geojson", layer="OGRGeoJSON")
world <- world[!world$iso_a3 %in% c("ATA"),]
world <- spTransform(world, CRS("+proj=wintri"))
 
map_w <- ggplot2::fortify(world, region="iso_a3")
 
# really quick way to get coords from a KML file
 
launch_sites <- rbindlist(lapply(ogrListLayers("data/launch-sites.kml")[c language="(1:2,4:9)"][/c], function(layer) {
  tmp <- readOGR("data/launch-sites.kml", layer)
  places <- data.table(coordinates(tmp)[,1:2], as.character(tmp$Name))
}))
setnames(launch_sites, colnames(launch_sites), c("lon", "lat", "name"))
 
# now, project the coordinates we extracted
 
coordinates(launch_sites) <-  ~lon+lat
launch_sites <- as.data.frame(SpatialPointsDataFrame(spTransform(
  SpatialPoints(launch_sites, CRS("+proj=longlat")), CRS("+proj=wintri")),
  launch_sites@data))
 
map_w %>%
  group_by(group, id) %>%
  ggvis(~long, ~lat) %>%
  layer_paths(fill:="#252525", stroke:="white", strokeOpacity:=0.5, strokeWidth:=0.25) %>%
  layer_points(data=launch_sites, 
               x=~lon, y=~lat, 
               fill:="#cb181d", stroke:="white", 
               size:=25, fillOpacity:=0.5, strokeWidth:=0.25) %>%
  hide_legend("fill") %>%
  hide_axis("x") %>% hide_axis("y") %>%
  set_options(width=900, height=500, keep_aspect=TRUE)

The main differences in this example are the re-projection of the data we’re using. I grabbed a KML file of rocket launch sites from Wikipedia and made it into a data frame then [re]project those points into Winkel-Tripel for use with Winkel-Tripel world map made at the beginning of the example. The ggplot coord_map handles these transforms for you, so until there’s a ggvis equivalent, you’ll need to do it this way (though, there’s not Winkel-Tripel projection in the mapproject package so you kinda need to do it this way for ggplot as well for this projection).

Wrapping Up

There’s /code for the “normal”, Rmd and Shiny versions of these examples. Give each a go and try tweaking various parameters, changing up the tooltips or using your own data. Don’t forget to drop a note in the comments with any of your creations and use github for any code issues.

To leave a comment for the author, please follow the link and comment on their blog: rud.is » R.

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