Lesson 4 Visualize: ggplot2, plotly, tmap

4.1 Plot

Inspiring people:

• Hadley Wickham: grammar of graphics

  

• Hans Rosling: Gapminder

  

  Gapminder World - Wealth & Health of Nations

  

4.1.1 Static: ggplot

• Creating publication quality graphics - Software Carpentry

4.1.1.1 Scatterplot

library(dplyr)
library(ggplot2)
library(gapminder)

# preview data
gapminder

# get range of available data
summary(gapminder)

# setup dataframe
g = gapminder %>%
  filter(year==2007) %>%   # most recent year 
  mutate(pop_m = pop/1e6)  # population, millions

# plot scatterplot of most recent year 
s = ggplot(g, aes(x=gdpPercap, y=lifeExp)) +
  geom_point()
s

# add aesthetic of size by population
s = s + 
  aes(size=pop_m)
s

# add aesthetic of color by continent
s = s + 
  aes(color=continent)
s

# add title, update axes labels
s = s + 
  ggtitle('Health & Wealth of Nations for 2007') +
  xlab('GDP per capita ($/year)') +
  ylab('Life expectancy (years)')
s

# label legend
s = s + 
  scale_colour_discrete(name='Continent') +
  scale_size_continuous(name='Population (M)')
s

Your Turn

Now with country emissions datasets…

• CO2 Emissions from Fossil Fuels since 1751, By Nation - Dataset - Frictionless Open Data
• datasets/gdp

4.1.1.2 Boxplot

# boxplot by continent
b = ggplot(g, aes(x=continent, y=lifeExp)) +
  geom_boxplot()
b

# match color to continents, like scatterplot
b = b +
  aes(fill=continent)
b

# drop legend, add title, update axes labels
b = b +
  theme(legend.position='none') +
  ggtitle('Life Expectancy by Continent for 2007') +
  xlab('Continent') +
  ylab('Life expectancy (years)')
b

Your Turn: Make a similar plot but for gdpPercap. Be sure to update the plot’s aesthetic, axis label and title accordingly.

4.1.2 Interactive: plotly

ggplot2 | plotly

library(plotly) # install.packages('plotly')

# scatterplot (Note: key=country shows up on rollover)
s = ggplot(g, aes(x=gdpPercap, y=lifeExp, key=country)) +
  geom_point()
ggplotly(s)

# boxplot
ggplotly(b)

Your Turn: Expand the interactive scatterplot to include all the other bells and whistles of the previous plot in one continuous set of code (no in between setting of s).

4.1.3 Interactive: Exploding Boxplot

library(explodingboxplotR) # devtools::install_github('timelyportfolio/explodingboxplotR')

exploding_boxplot(g,
  y = 'lifeExp',
  group = 'continent',
  color = 'continent',
  label = 'country')

4.1.4 Interactive: Motion Plot

The googleVis package ports most of the Google charts functionality.

For every R chunk must set option results='asis', and once before any googleVis plots, set op <- options(gvis.plot.tag='chart').

• Rmarkdown and googleVis

• googleVis examples

suppressPackageStartupMessages({
  library(googleVis) # install.packages('googleVis')
})

## Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

op <- options(gvis.plot.tag='chart')

m = gvisMotionChart(
  gapminder %>%
    mutate(
      pop_m = pop / 1e6,
      log_gdpPercap = log(gdpPercap)), 
  idvar='country', 
  timevar='year', 
  xvar='log_gdpPercap', 
  yvar='lifeExp', 
  colorvar='continent',
  sizevar='pop_m')
plot(m)

Your Turn: Repeat the motion chart with the country having the highest gdpPercap filtered out.

4.2 Map

Thematic maps tmap:

• tmap in a nutshell
• tmap modes: plot and interactive view

4.2.1 Static

library(sf)
library(tmap) # install.packages('tmap')

# load world spatial polygons
data(World)

# inspect values in World
World %>% st_set_geometry(NULL)

# gapminder countries not in World. skipping for now
g %>% 
  anti_join(World, by=c('country'='name')) %>% 
  arrange(desc(pop))

# World countries not in gapminder. skipping for now
World %>% 
  anti_join(g, by=c('name'='country')) %>% 
  arrange(desc(pop_est)) %>%
  select(iso_a3, name, pop_est)

# join gapminder data to World
World = World %>%
  left_join(g, by=c('name'='country'))

# make map
m = tm_shape(World) +
    tm_polygons('lifeExp', palette='RdYlGn', id='name', title='Life expectancy (years)', auto.palette.mapping=F) +
    tm_style_gray() + tm_format_World()

## Warning: The argument auto.palette.mapping is deprecated. Please use
## midpoint for numeric data and stretch.palette for categorical data to
## control the palette mapping.

## Warning in tm_style_gray(): tm_style_gray is deprecated as of tmap version
## 2.0. Please use tm_style("gray", ...) instead

## Warning in tm_format_World(): tm_format_World is deprecated as of tmap
## version 2.0. Please use tm_format("World", ...) instead

m

4.2.2 Interactive

# show interactive map
tmap_leaflet(m)

4.3 References

• ggplot2-cheatsheet-2.0.pdf
• Interactive Plots and Maps - Environmental Informatics
• Graphs with ggplot2 - Cookbook for R
• ggplot2 Essentials - STHDA
• NEON Working with Geospatial Data