In RStudio, I have produced a leaflet map using tmap_leaflet function where some polygons are coloured depending on the value of a variable and on top of the polygons some grobs are printed which show the breakdown of the value of the variable into three categories. I want this to be a part of an Rmd file which is knitted fine and the output is correct in the RStudio popup window but in the automatically saved html file the grobs are missing.
Here is a reproducible example of my Rmd file written in R studio:
knitr::opts_chunk$set(echo = FALSE)
library(tigris) #to download a USA map
library(sf)
library(dplyr)
library(tmap) #to build the map
library(tmaptools) #for function append_data
library(ggplot2) #to produce the grobs
library(leaflet) # for setView function
#download the usa map shapefile as an sf file
us_geo <- states(class = "sf")
#keep only the 48 contiguous States of the US which will be the background of the map
us48_geo <- subset(us_geo, !(NAME %in% c("Alaska",
"Hawaii",
"Puerto Rico",
"Commonwealth of the Northern Mariana Islands",
"United States Virgin Islands" ,
"Guam",
"American Samoa"
)) )
#data I want to plot on the map for four states
#the colour of the polygons of these States will depend on the value of Total_Number
#the grob for each state will be a pie chart showing the breakdown of the total number in the three categories, the percentages of which are also provided
dat_df <- data.frame( STATE = c("WA", "CA", "FL", "NJ"),
Total_Number = c(800, 1200, 1700, 2100),
Perc_Cat1 = c(30, 40, 50, 60),
Perc_Cat2 = c(10, 20, 30, 10),
Perc_Cat3 = c(60, 40, 20, 30))
#create an sf object for the four states I have data for
usStates_sf <- us48_geo %>%
filter(STUSPS %in% c("WA", "CA", "FL", "NJ") ) %>%
append_data(dat_df, key.shp = "STUSPS", key.data = "STATE")
#to make grobs, data need to be in long format
dat_df_long <-reshape(dat_df,
varying = list(3:5),
timevar = "Category",
v.names = "Perc",
idvar = "STATE",
direction="long")
#Category needs to be defined as factor so that scale_fill_manual() in ggplot() works as intended
dat_df_long$Category <- factor(dat_df_long$Category, levels = 1:3)
#define the colours of the piechart
cat_cols <- get_brewer_pal("Set3", 3)
#make the grobs
grobs <- lapply( split(dat_df_long,
dat_df_long$STATE), function(x) {
ggplotGrob( ggplot(x, aes(x="", y=-Perc, fill= Category)) +
geom_bar(width=1, stat="identity") +
scale_y_continuous(expand=c(0,0)) +
scale_fill_manual( values = cat_cols) +
theme_ps(plot.axes = FALSE) +
coord_polar("y", start=0) #to transform bar to pie
)
})
#to produce a static map
static_map <-
#background of the map:
tm_shape(us48_geo) + tm_polygons( col="white") +
#polygons of the four states I have data for coloured depending on the value of Total_Number
tm_shape(usStates_sf) +
tm_polygons(col="Total_Number",
palette = "YlOrBr",
title ="Total Number",
contrast = 0.7,
id = "STUSPS",
popup.vars = c("Total Number" = "Total_Number")) +
#add the grobs (piecharts) for each State
tm_symbols(shape="STUSPS",
shapes=grobs,
scale=1.5,
legend.shape.show = FALSE,
legend.size.is.portrait = TRUE,
shapes.legend = 22,
id = "STUSPS",
popup.vars = c("Category 1 (%)" ="Perc_Cat1",
"Category 2 (%)" = "Perc_Cat2",
"Category 3 (%)" = "Perc_Cat3") ) +
tm_add_legend(type="fill",
col=cat_cols,
labels= levels(dat_df_long$Category),
title="Category") +
tm_layout(legend.stack = "horizontal" )
#render the static map into a leaflet map
leafletmap <- tmap_leaflet(static_map) %>% setView(-96, 37.8, zoom=4)
The map to be plotted is the one below
leafletmap
Everything works fine in RStudio but the grobs are missing in the html file saved automatically in my working folder.
