Multivariate Data Visualization with R

Name: Multivariate Data Visualization with R
Rating: 4.3 (42 reviews)

Course describes and demonstrates a creative approach for constructing and drawing grid-based multivariate graphs in R

Created byGeoffrey Hubona, Ph.D.

Last updated 7/2020

English

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What you'll learn

Graphically depict visual 2D, 3D, 4D (and so on) relationships that exist in multivariate data sets.
Understand how "trellis" graphic objects are different from other graphic objects in R.
Understand how to apply the techniques of conditioning and paneling to present multivariate data relationships.
Understand the nature of lattice panel functions and know how to create and modify them for brilliant multivariate graphics displays.
Have a powerful visual toolset to visually present the results of multi-variable statistical model fitting.

Course content

4 sections • 32 lectures • 6h 45m total length

Introduction to Course1:16
Dr. Jeffrey hewe Bona introduces multivariate data plots in R using trellised graphics, conditioning and panel functions to visualize models with three or more variables.
Introduction to Lattice16:24
The lattice package, written by Deepayan Sarkar, attempts to improve on base R graphics by providing better defaults and the ability to easily display multivariate relationships. In particular, the package supports the creation of trellis graphs - graphs that display a variable or the relationship between variables, conditioned on one or more other variables.

The typical format is

<em>graph_type</em>(<em>formula</em>, data=)

where graph_type is selected from the listed below. formula specifies the variable(s) to display and any conditioning variables . For example ~x|A means display numeric variable x for each level of factor A.y~x | A*B means display the relationship between numeric variables y and x separately for every combination of factor A and B levels. ~x means display numeric variable x alone.
The Trellis Object13:18
A trellis object, as returned by high level lattice functions like xyplot, is a list with the "class" attribute set to "trellis". Many of the components of this list are simply the arguments to the high level function that produced the object. Among them are: as.table, layout, page, panel, prepanel,main, sub, par.strip.text, strip, skip, xlab ylab, par.settings, lattice.options and plot.args.
Dimension and Physical Layout14:00
Learn to optimize lattice plots in R by transposing panel matrices, adjusting aspect, and using layout, between, and autokey to improve spacing, legends, and group displays.
Scales and Axes8:43
Explore how to set scales and axes in trellis plots, including panel conditioning, independent scales, and panel functions using the Titanic data to visualize survival by class, age, and sex.
Visualizing Univariate Distributions (part 1)17:04
In statistics, a univariate distribution is a probability distribution of only one random variable. This is in contrast to a multivariatedistribution, the probability distribution of a random vector (consisting of multiple random variables).
Visualizing Univariate Distributions (part 2)14:56
Explore univariate distribution visualization with Lavis plots and normal Q-Q plots, compare data to theoretical distributions, assess skewness and variance, and apply Box-Cox transformations to improve normality.
Two-Sample QQ Plots14:14
A q-q plot is a plot of the quantiles of the first data set against the quantiles of the second data set. By a quantile, we mean the fraction (or percent) of points below the given value. That is, the 0.3 (or 30%) quantile is the point at which 30% percent of the data fall below and 70% fall above that value.
Strip Plots8:03
Box-and-whisker plots summarize the data using a few quantiles, and possibly some outliers. This summarizing can be important when the number of observations is large. When the number of observations per sample is small, it is often sufficient to simply plot the sample values side by side in a common scale. Such plots are known as strip plots, also referred to as univariate scatter plots. They are in fact very similar to the bivariate scatter plots.

Multiway Tables12:16
An important subset of statistical data comes in the form of tables. Tables usually record the frequency or proportion of observations that fall into a particular category or combination of categories. They could also encode some other summary measure such as a rate (of binary events) or mean (of a continuous variable). In R, tables are usually represented by arrays of one (vectors), two (matrices), or more dimensions. To distinguish them from other vectors and arrays, they often have class “table”. The R functions table() and xtabs() can be used to create tables from raw data.
Multipanel Dot Plots11:09
Create multipanel dot plots in R to compare proportions across fields, using panel order and abbreviations to highlight differences. Adjust label length and independent axis rotation to enhance interpretation.
Scatter Plots and Extensions13:37
A scatter plot graphs two variables directly against each other in a Cartesian coordinate system. It is a simple graphic in the sense that the data are directly encoded without being summarized in any way; often the aspects that the user needs to worry about most are graphical ones such as whether to join the points by a line, what colors to use, and so on. Depending on the purpose, scatter plots can also be enhanced in several ways. In this chapter, we go over some of the variants supported by panel.xyplot(), which is the default panel function for both xyplot() and splom() (under the alias panel.splom()).
Shingles and Advanced Indexing6:34
Apply shingles and equal-count binning in R to analyze earthquake magnitudes across four panels, using a panel function and color subscripts to reveal overlaps and depth patterns.
More Scatter Plots (part 1)16:08
Explore quake data visuals by advancing from original plots to panel and x y plots, color-coding depth and magnitude, and adding a legend with lattice's groups and level colors.
More Scatter Plots (part 2)10:22
Plot three panels of acceleration by distance conditioned on earthquake magnitude, add a regression line and Loek smoothing, then explore panel functions and dual scales using the Seattle weather data.
Scatter Plot Matrices13:39
Scatter-plot matrices, produced by splom(), are exactly what the name suggests; they are a matrix of pairwise scatter plots given two or more variables. Conditioning is possible, but it is more common to call splom() with a data frame as its first argument.
Parallel Coordinates Plot7:29
Like scatter-plot matrices, parallel coordinates plots are hypervariate in nature, that is, they show relationships between an arbitrary number of variables. Their design is related to univariate scatter plots; in fact, they are basically univariate scatter plots of all variables of interest stacked parallel to each other (vertically in the implementation in lattice), with values that correspond to the same observation linked by line segments.

Trivariate Displays9:01
Trivariate displays encode three primary variables in a panel. There are four high-level functions in lattice that produce trivariate displays: cloud() creates three-dimensional scatter plots of unstructured trivariate data, whereas levelplot(), contourplot(), and wireframe() render surfaces or two dimensional tables evaluated on a systematic rectangular grid. Of these, cloud() and wireframe() are similar in that they both create two-dimensional projections of three-dimensional constructs, and they share several common arguments that control the details of the projection.
3D Scatter Plots (part 1)9:56
We begin with cloud(), which produces three-dimensional scatter plots. Most of the discussion in this section about projection and how to control it in cloud() applies to wireframe() as well.
3D Scatter Plots (part 2)8:38
Explore 3D scatter plots of earthquake epicenters by rotating the viewpoint to convey depth in a static display. Use multi-view panels and stereo-like viewing to simulate depth cues.
3D Panel Functions17:08
Explore 3d panel functions in lattice cloud, using type values like H to create quasi three-dimensional bar charts and 3d scatter plots, and preview wireframe, level, and contour plots.
Visualizing 3D Surfaces13:52
More 3D Visualizations16:50
Visualizing Theoretical 3D Surfaces13:39
The methods we used to plot regression surfaces using wireframe() can be easily adapted to mathematical surfaces.

Graphical Parameters and Other Settings15:05
Graphical parameters are often critical in determining the effectiveness of a plot. Such parameters include obvious ones such as colors, symbols, line types, and fonts for the various elements of a graph, as well as more subtle ones such as the length of tick marks or the amount of space separating different components of the graph. The parameters used in lattice displays are highly customizable. Many of them can be controlled directly by specifying suitable arguments in a high-level function call. Most derive their default values from a system of common global settings that can also be modified by the user. The latter approach has two primary benefits: it allows good global defaults to be specified, and it provides a consistent “look and feel” to lattice graphics while letting the user retain ultimate control.
Graphical Parameters Continued14:15
Explore how to recreate plots by updating par settings to adjust transparency, color, line width, and plot outlines, then examine lattice graphics, panels, and axis controls in trellis displays.
Plot Coordinates and Axis Annotation13:19
Learn to plot coordinates and annotate axes in R, reverse axis limits, adjust aspect ratio, and customize tick marks and labels with pre-painted and custom scales for various data.
Labels and Legends14:49
Data Manipulation (part 1)13:56
Data Manipulation (part 2)15:27
Master data manipulation for multivariate visualization with latus by using subset expressions, x y plots, and conditioned panels across beaver, age, and quake data.
Shingles and Related Utilities14:57
Explore lattice plots, including box and whisker plots with shingles, square-root transforms of stations, and strip annotations. Learn coercion of numeric variables to shingles and cut-and-stack time series plots.
Ordering Categorical Variables14:59
Learn how to reorder categorical variable levels in R to improve the visual clarity of lattice plots, using the reorder function, and see how this affects panels, densities, and strips.

Requirements

Students will need to install R and RStudio (instructions are provided in the course materials).

Description

It is often both useful and revealing to create visualizations, plots and graphs of the multivariate data that is the subject of one's research project. Often, both pre-analysis and post-analysis visualizations can help one understand “what is going on in the data" in a way that looking at numerical summaries of fitted model estimates cannot. The lattice package in R is uniquely designed to graphically depict relationships in multivariate data sets.

This course describes and demonstrates this creative approach for constructing and drawing grid-based multivariate graphic plots and figures using R. Lattice graphics are characterized as multi-variable (3, 4, 5 or more variables) plots that use conditioning and paneling. Consequently, it is a popular approach for, and a good fit to visually present the results of multi-variable statistical model fitting. The appearance of most of the plots, graphs and figures are determined by panel functions, rather than by the high-level graphics function calls themselves. Further, the user of lattice graphics has extensive and comprehensive control over many more of the details and features of the visual plots, far greater control that is afforded by the base graphics approach in R. The method is based on trellis graphics which were popularized in the S language developed by Bell Labs.

Who this course is for:

Anyone who uses R, or who wants to use R, for any sort of multivariate data analysis would benefit from taking this course.
The course is appropriate for students, scientists, or other quantitative-analysis professionals who want to display numerical information in plots and graphs.
To take advantage of the course, students will need to have a basic (introductory) level or ability to use R software. However, all of the graphic R scripts are provided with the course materials.

Multivariate Data Visualization with R

What you'll learn

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Course content

Introduction to Lattice and to "Trellis" Graphics9 lectures • 1hr 48min

Multiway Tables and Scatter Plots8 lectures • 1hr 31min

Trivariate, 3D, and Other Complex Displays7 lectures • 1hr 29min

Finer Control Graphical Parameters and Other Settings8 lectures • 1hr 57min

Requirements

Description

Who this course is for: