Hands-on Exercise 5.4: Visual Multivariate Analysis with Parallel Coordinates Plot

1 Getting Started

1.1 Install and loading R packages.

pacman::p_load(GGally, parallelPlot, tidyverse)

1.2 Importing the data

wh <- read_csv("../../data/WHData-2018.csv")

2 Plotting Static Parallel Coordinates Plot

2.1 Plotting a simple parallel coordinates

ggparcoord(data = wh, 
           columns = c(7:12))

Notice that only two argument namely data and columns is used. Data argument is used to map the data object (i.e. wh) and columns is used to select the columns for preparing the parallel coordinates plot.

2.2 Plotting a parallel coordinates with boxplot

ggparcoord(data = wh, 
           columns = c(7:12), 
           groupColumn = 2,
           scale = "uniminmax",
           alphaLines = 0.2,
           boxplot = TRUE, 
           title = "Parallel Coordinates Plot of World Happines Variables")

Things to learn from the code chunk above.

• groupColumn argument is used to group the observations (i.e. parallel lines) by using a single variable (i.e. Region) and colour the parallel coordinates lines by region name.

• scale argument is used to scale the variables in the parallel coordinate plot by using uniminmax method. The method univariately scale each variable so the minimum of the variable is zero and the maximum is one.

• alphaLines argument is used to reduce the intensity of the line colour to 0.2. The permissible value range is between 0 to 1.

• boxplot argument is used to turn on the boxplot by using logical TRUE. The default is FALSE.

• title argument is used to provide the parallel coordinates plot a title.

2.3 Parallel coordinates with facet

Since ggparcoord() is developed by extending ggplot2 package, we can combination use some of the ggplot2 function when plotting a parallel coordinates plot.

In the code chunk below, facet_wrap() of ggplot2 is used to plot 10 small multiple parallel coordinates plots. Each plot represent one geographical region such as East Asia.

ggparcoord(data = wh, 
           columns = c(7:12), 
           groupColumn = 2,
           scale = "uniminmax",
           alphaLines = 0.2,
           boxplot = TRUE, 
           title = "Multiple Parallel Coordinates Plots of World Happines Variables by Region") +
  facet_wrap(~ Region)

One of the aesthetic defect of the current design is that some of the variable names overlap on x-axis.

2.4 Rotating x-axis text label

To make the x-axis text label easy to read, let us rotate the labels by 30 degrees. We can rotate axis text labels using theme() function in ggplot2 as shown in the code chunk below

ggparcoord(data = wh, 
           columns = c(7:12), 
           groupColumn = 2,
           scale = "uniminmax",
           alphaLines = 0.2,
           boxplot = TRUE, 
           title = "Multiple Parallel Coordinates Plots of World Happines Variables by Region") +
  facet_wrap(~ Region) + 
  theme(axis.text.x = element_text(angle = 30))

Thing to learn from the code chunk above:

• To rotate x-axis text labels, we use axis.text.x as argument to theme() function. And we specify element_text(angle = 30) to rotate the x-axis text by an angle 30 degree.

2.5 Adjusting the rotated x-axis text label

Rotating x-axis text labels to 30 degrees makes the label overlap with the plot and we can avoid this by adjusting the text location using hjust argument to theme’s text element with element_text(). We use axis.text.x as we want to change the look of x-axis text.

ggparcoord(data = wh, 
           columns = c(7:12), 
           groupColumn = 2,
           scale = "uniminmax",
           alphaLines = 0.2,
           boxplot = TRUE, 
           title = "Multiple Parallel Coordinates Plots of World Happines Variables by Region") +
  facet_wrap(~ Region) + 
  theme(axis.text.x = element_text(angle = 30, hjust=1))

3 Plotting Interactive Parallel Coordinates Plot: parallelPlot methods

parallelPlot is an R package specially designed to plot a parallel coordinates plot by using ‘htmlwidgets’ package and d3.js. In this section, you will learn how to use functions provided in parallelPlot package to build interactive parallel coordinates plot.

3.1 The basic plot

The code chunk below plot an interactive parallel coordinates plot by using parallelPlot().

wh <- wh %>%
  select("Happiness score", c(7:12))
parallelPlot(wh,
             width = 320,
             height = 250)

Notice that some of the axis labels are too long. You will learn how to overcome this problem in the next step.

3.2 Rotate axis label

In the code chunk below, rotateTitle argument is used to avoid overlapping axis labels.

One of the useful interactive feature of parallelPlot is we can click on a variable of interest, for example Happiness score, the monotonous blue colour (default) will change a blues with different intensity colour scheme will be used.

parallelPlot(wh,
             rotateTitle = TRUE)

3.3 Changing the colour scheme

We can change the default blue colour scheme by using continousCS argument as shown in the code chunk below.

parallelPlot(wh,
             continuousCS = "YlOrRd",
             rotateTitle = TRUE)

3.4 Parallel coordinates plot with histogram

In the code chunk below, histoVisibility argument is used to plot histogram along the axis of each variables.

histoVisibility <- rep(TRUE, ncol(wh))
parallelPlot(wh,
             rotateTitle = TRUE,
             histoVisibility = histoVisibility)