Data Visualization in R

Le Yan

2018-04-04

Disclaimer

Slides were written with Rmarkdown and R Shiny
- Built from a source file that mixes texts and R code chunks
  - https://rmarkdown.rstudio.com/
- R Shiny enables interactive content
  - https://shiny.rstudio.com/
No hands-on exercises, but all code segments can be executed in Rstudio, so you can play along if you’d like to

R Graphic Systems

There are at least three plotting systems in R
- base
- lattice
- ggplot2
Today we will touch on base briefly then focus on ggplot2

Outline

base plot system
ggplot2 plot system
- Basic concepts
- Geom and stat functions
- Title, axis labels and legends
- Themes
- Scale functions
- Coordination systems
- Faceting
Brief introduction to interactive visualization

DataSets

Datasets are from the packages datasets, gcookbook and ggplot2
To learn more about those datasets, run help(library='<name>')
For information on individual datasets, run ?<name of dataset>

library(help='datasets')

        Information on package 'datasets'

Description:

Package:       datasets
Version:       3.3.3
Priority:      base
Title:         The R Datasets Package
Author:        R Core Team and contributors worldwide
Maintainer:    R Core Team <R-core@r-project.org>
Description:   Base R datasets.
License:       Part of R 3.3.3
Built:         R 3.3.3; ; 2017-03-06 14:15:22 UTC; windows

Index:

AirPassengers           Monthly Airline Passenger Numbers 1949-1960
BJsales                 Sales Data with Leading Indicator
BOD                     Biochemical Oxygen Demand
CO2                     Carbon Dioxide Uptake in Grass Plants
ChickWeight             Weight versus age of chicks on different diets
DNase                   Elisa assay of DNase
EuStockMarkets          Daily Closing Prices of Major European Stock
...

First Plot in R

We will use the “pressure” dataset for our first plot.

First, let’s examine the data:

str(pressure)

## 'data.frame':    19 obs. of  2 variables:
##  $ temperature: num  0 20 40 60 80 100 120 140 160 180 ...
##  $ pressure   : num  0.0002 0.0012 0.006 0.03 0.09 0.27 0.75 1.85 4.2 8.8 ...

summary(pressure)

##   temperature     pressure       
##  Min.   :  0   Min.   :  0.0002  
##  1st Qu.: 90   1st Qu.:  0.1800  
##  Median :180   Median :  8.8000  
##  Mean   :180   Mean   :124.3367  
##  3rd Qu.:270   3rd Qu.:126.5000  
##  Max.   :360   Max.   :806.0000

?pressure

pressure {datasets} R Documentation
Vapor Pressure of Mercury as a Function of Temperature

Description

Data on the relation between temperature in degrees Celsius and vapor pressure of mercury in millimeters (of mercury).

Usage

pressure
Format

A data frame with 19 observations on 2 variables.

[, 1]    temperature     numeric     temperature (deg C)
[, 2]    pressure    numeric     pressure (mm)
Source

Weast, R. C., ed. (1973) Handbook of Chemistry and Physics. CRC Press.

References

McNeil, D. R. (1977) Interactive Data Analysis. New York: Wiley.

First Plot in R

We can use the plot() function in the base plot system to create a scatter plot:

# Simply specify the x and y variables.
plot(pressure$temperature,pressure$pressure)

R image

Since there are only two variables, we can simply run:

plot(pressure)

R image

More Plot Types

The type argument of plot() can be used to specify plot type
- “p” for “point”
- “l” for “line”
- “b” for “both”

plot(pressure, type="<name of type>")

Shiny applications not supported in static R Markdown documents

Adding More Layers

There are a few functions that can be used to add more elements/layers to the plot
- points
- lines
- texts

# Create the plot with title and axis labels.
plot(pressure,type="l",
     main="Vapor Pressure of Mercury",
     xlab="Temperature", 
     ylab="Vapor Pressure")
# Add points
points(pressure,col='red') 
# Add annotation
text(150,700,"Source: Weast, R. C., ed. (1973) Handbook \n
     of Chemistry and Physics. CRC Press.")

R image

Boxplot

Use boxplot() for boxplots

dataset:

str(mpg)

## Classes 'tbl_df', 'tbl' and 'data.frame':    234 obs. of  11 variables:
##  $ manufacturer: chr  "audi" "audi" "audi" "audi" ...
##  $ model       : chr  "a4" "a4" "a4" "a4" ...
##  $ displ       : num  1.8 1.8 2 2 2.8 2.8 3.1 1.8 1.8 2 ...
##  $ year        : int  1999 1999 2008 2008 1999 1999 2008 1999 1999 2008 ...
##  $ cyl         : int  4 4 4 4 6 6 6 4 4 4 ...
##  $ trans       : chr  "auto(l5)" "manual(m5)" "manual(m6)" "auto(av)" ...
##  $ drv         : chr  "f" "f" "f" "f" ...
##  $ cty         : int  18 21 20 21 16 18 18 18 16 20 ...
##  $ hwy         : int  29 29 31 30 26 26 27 26 25 28 ...
##  $ fl          : chr  "p" "p" "p" "p" ...
##  $ class       : chr  "compact" "compact" "compact" "compact" ...

summary(mpg)

##  manufacturer          model               displ            year     
##  Length:234         Length:234         Min.   :1.600   Min.   :1999  
##  Class :character   Class :character   1st Qu.:2.400   1st Qu.:1999  
##  Mode  :character   Mode  :character   Median :3.300   Median :2004  
##                                        Mean   :3.472   Mean   :2004  
##                                        3rd Qu.:4.600   3rd Qu.:2008  
##                                        Max.   :7.000   Max.   :2008  
##       cyl           trans               drv                 cty       
##  Min.   :4.000   Length:234         Length:234         Min.   : 9.00  
##  1st Qu.:4.000   Class :character   Class :character   1st Qu.:14.00  
##  Median :6.000   Mode  :character   Mode  :character   Median :17.00  
##  Mean   :5.889                                         Mean   :16.86  
##  3rd Qu.:8.000                                         3rd Qu.:19.00  
##  Max.   :8.000                                         Max.   :35.00  
##       hwy             fl               class          
##  Min.   :12.00   Length:234         Length:234        
##  1st Qu.:18.00   Class :character   Class :character  
##  Median :24.00   Mode  :character   Mode  :character  
##  Mean   :23.44                                        
##  3rd Qu.:27.00                                        
##  Max.   :44.00

Boxplot

boxplot(hwy ~ cyl, data=mpg)

# Use the title function to add title and labels.
title("Highway Mileage per Gallon",
      xlab = "Number of cylinders",
      ylab = "Mileage (per gallon)")

R image

Histogram

Function hist() can used to create histograms

hist(mpg$hwy)