Scatter, Box, and Violin Plots

David Gerbing

lessR provides many versions of a scatter plot with its Plot() function for one or two variables with an option to provide a separate scatterplot for each level of one or two categorical variables. Access all scatterplots with the same simple syntax. The first variable listed without a parameter name, the x parameter, is plotted along the x-axis. Any second variable listed without a parameter name, the y parameter, is plotted along the y-axis. Each parameter may be represented by a continuous or categorical variable, a single variable or a vector of variables.

The Data

Illustrate with the Employee data included as part of lessR.

d <- Read("Employee")
## 
## >>> Suggestions
## Recommended binary format for data files: feather
##   Create with Write(d, "your_file", format="feather")
## More details about your data, Enter:  details()  for d, or  details(name)
## 
## Data Types
## ------------------------------------------------------------
## character: Non-numeric data values
## integer: Numeric data values, integers only
## double: Numeric data values with decimal digits
## ------------------------------------------------------------
## 
##     Variable                  Missing  Unique 
##         Name     Type  Values  Values  Values   First and last values
## ------------------------------------------------------------------------------------------
##  1     Years   integer     36       1      16   7  NA  7 ... 1  2  10
##  2    Gender character     37       0       2   M  M  W ... W  W  M
##  3      Dept character     36       1       5   ADMN  SALE  FINC ... MKTG  SALE  FINC
##  4    Salary    double     37       0      37   53788.26  94494.58 ... 56508.32  57562.36
##  5    JobSat character     35       2       3   med  low  high ... high  low  high
##  6      Plan   integer     37       0       3   1  1  2 ... 2  2  1
##  7       Pre   integer     37       0      27   82  62  90 ... 83  59  80
##  8      Post   integer     37       0      22   92  74  86 ... 90  71  87
## ------------------------------------------------------------------------------------------

As an option, lessR also supports variable labels. The labels are displayed on both the text and visualization output. Each displayed label consists of the variable name juxtaposed with the corresponding label. Create the table formatted as two columns. The first column is the variable name and the second column is the corresponding variable label. Not all variables need to be entered into the table. The table can be stored as either a csv file or an Excel file.

Read the variable label file into the l data frame, currently the only permissible name for the label file.

l <- rd("Employee_lbl")
## 
## >>> Suggestions
## Recommended binary format for data files: feather
##   Create with Write(d, "your_file", format="feather")
## More details about your data, Enter:  details()  for d, or  details(name)
## 
## Data Types
## ------------------------------------------------------------
## character: Non-numeric data values
## ------------------------------------------------------------
## 
##     Variable                  Missing  Unique 
##         Name     Type  Values  Values  Values   First and last values
## ------------------------------------------------------------------------------------------
##  1     label character      8       0       8   Time of Company Employment ... Test score on legal issues after instruction
## ------------------------------------------------------------------------------------------

Display the available labels.

l
##                                                label
## Years                     Time of Company Employment
## Gender                                  Man or Woman
## Dept                             Department Employed
## Salary                           Annual Salary (USD)
## JobSat            Satisfaction with Work Environment
## Plan             1=GoodHealth, 2=GetWell, 3=BestCare
## Pre    Test score on legal issues before instruction
## Post    Test score on legal issues after instruction

Continuous Variables

Two Variables

A typical scatterplot visualizes the relationship of two continuous variables, here Years worked at a company, and annual Salary. Following is the function call to Plot() for the default visualization.

Because d is the default name of the data frame that contains the variables for analysis, the data parameter that names the input data frame need not be specified. That is, no need to specify data=d, though this parameter can be explicitly included in the function call if desired.

Plot(Years, Salary)

## --- Pearson's product-moment correlation --- 
##  
## Years: Time of Company Employment 
## Salary: Annual Salary (USD) 
##  
## Number of paired values with neither missing, n = 36 
## Sample Correlation of Years and Salary: r = 0.852 
##   
## Hypothesis Test of 0 Correlation:  t = 9.501,  df = 34,  p-value = 0.000 
## 95% Confidence Interval for Correlation:  0.727 to 0.923 
## 

Enhance the default scatterplot with parameter enhance. The visualization includes the mean of each variable indicated by the respective line through the scatterplot, the 95% confidence ellipse, labeled outliers, least-squares regression line with 95% confidence interval, and the corresponding regression line with the outliers removed.

Plot(Years, Salary, enhance=TRUE)
## [Ellipse with Murdoch and Chow's function ellipse from their ellipse package]

## --- Pearson's product-moment correlation --- 
##  
## Years: Time of Company Employment 
## Salary: Annual Salary (USD) 
##  
## Number of paired values with neither missing, n = 36 
## Sample Correlation of Years and Salary: r = 0.852 
##   
## Hypothesis Test of 0 Correlation:  t = 9.501,  df = 34,  p-value = 0.000 
## 95% Confidence Interval for Correlation:  0.727 to 0.923 
##   
## 
## >>> Outlier analysis with Mahalanobis Distance 
##  
##   MD  ID 
## ----- ----- 
## 8.14  18 
## 7.84  34 
##  
## 5.63  31 
## 5.58  19 
## 3.75   4 
## ...  ...

A variety of fit lines can be plotted. The available values: "loess" for general non-linear fit, "lm" for linear least squares, "null" for the null (flat line) model, "exp" for the exponential growth and decay, "quad" for the quadratic model, and power for the general power beyond 2. Setting fit to TRUE plots the "loess" line. With the value of power, specify the value of the root with parameter fit_power.

Here, plot the general non-linear fit. For emphasis set plot_errors to TRUE to plot the residuals from the line. The sum of the squared errors is displayed to facilitate the comparison of different models.

Plot(Years, Salary, fit="loess", plot_errors=TRUE)

## 
## Fit: Mean Squared Error, MSE = 100,834,065
## 

Next, plot the exponential fit and show the residuals from the exponential curve. These data are approximately linear so the exponential curve does not vary far from a straight line. The function displays the corresponding sum of squared errors to assist in comparing various models to each other.

Plot(Years, Salary, fit="exp", plot_errors=TRUE)

## 
##  Regressed linearized data of transformed data values of Salary with log() 
##  For predicted values, back transform with exp() of regression model
## 
##  Line: b0 = 10.777   b1 = 0.041    Fit: MSE = 0.022   Rsq = 0.722
## 

The parameter transforms the y variable to the specified power from the default of 1 before doing the regression analysis. The availability of this parameter provides for a wide range of modifications to the underlying functional form of the fit curve.

Three Variables

Map a continuous variable, such as Pre, to the plotted points with the size parameter, a bubble plot.

Plot(Years, Salary, size=Pre)

## --- Pearson's product-moment correlation --- 
##  
## Years: Time of Company Employment 
## Salary: Annual Salary (USD) 
##  
## Number of paired values with neither missing, n = 36 
## Sample Correlation of Years and Salary: r = 0.852 
##   
## Hypothesis Test of 0 Correlation:  t = 9.501,  df = 34,  p-value = 0.000 
## 95% Confidence Interval for Correlation:  0.727 to 0.923 
##   
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## radius: 0.12    size of largest bubble 
## power: 0.50     relative bubble sizes

Indicate multiple variables to plot along either axis with a vector defined according to the base R function c(). Plot the linear model for each variable according to the fit parameter set to "lm". By default, when multiple lines are plotted on the same panel, the confidence interval is turned off by internally setting the parameter fit_se set to 0. Explicitly override this parameter value as needed.

Plot(c(Pre, Post), Salary, fit="lm", fit_se=0)

## --- Pearson's product-moment correlation --- 
##  
## Post: Test score on legal issues after instruction 
## Salary: Annual Salary (USD) 
##  
## Number of paired values with neither missing, n = 37 
## Sample Correlation of Post and Salary: r = -0.070 
##   
## Hypothesis Test of 0 Correlation:  t = -0.416,  df = 35,  p-value = 0.680 
## 95% Confidence Interval for Correlation:  -0.385 to 0.260 
## 

Scatterplot Matrix

Multiple variables for the first parameter value, x, and no values for y, plot as a scatterplot matrix. Pass a single vector, such as defined by c(). Request the non-linear fit line and corresponding confidence interval by specifying TRUE or loess for the fit parameter. Request a linear fit line with the value of "lm".

Plot(c(Salary, Years, Pre, Post), fit="lm")

Smoothed and Binned Scatterplots

Smoothing and binning are two procedures for visualizing a relationship with many data values.

To obtain a larger data set, in this example generate random data with base R rnorm(), then plot. Plot() first checks the presence of the specified variables in the global environment (workspace). If not there, then from a data frame, of which the default value is d. Here, randomly generate values from normal populations for x and y in the workspace.

set.seed(13)
x=rnorm(4000)
y= 8*x + rnorm(4000,1, 30)
Plot(x, y)
## >>> Note: x is not in a data frame (table)
## >>> Note: y is not in a data frame (table)

## --- Pearson's product-moment correlation --- 
##  
## Number of paired values with neither missing, n = 4000 
## Sample Correlation of x and y: r = 0.251 
##   
## Hypothesis Test of 0 Correlation:  t = 16.397,  df = 3998,  p-value = 0.000 
## 95% Confidence Interval for Correlation:  0.222 to 0.280 
## 

With large data sets, even for continuous variables there can be much over-plotting of points. One strategy to address this issue smooths the scatterplot by turning on the smooth parameter. The individual points superimposed on the smoothed plot are potential outliers. The default number of plotted outliers is 100. Turn off the plotting of outliers completely by setting parameter smooth_points to 0. Show the linear trend with fit set to "lm".

Plot(x, y, smooth=TRUE, fit="lm")
## >>> Note: x is not in a data frame (table)
## >>> Note: y is not in a data frame (table)

## --- Pearson's product-moment correlation --- 
##  
## Number of paired values with neither missing, n = 4000 
## Sample Correlation of x and y: r = 0.251 
##   
## Hypothesis Test of 0 Correlation:  t = 16.397,  df = 3998,  p-value = 0.000 
## 95% Confidence Interval for Correlation:  0.222 to 0.280 
##   
## 
##  Line: b0 = 1.030687568   b1 = 7.919636637    Fit: MSE = 917.032   Rsq = 0.063
## 

Another strategy for alleviating over-plotting makes the fill color mostly transparent with the transparency parameter, or turn off completely by setting fill to "off". The closer the value of trans is to 1, the more transparent is the fill.

Plot(x, y, transparency=0.95)
## >>> Note: x is not in a data frame (table)
## >>> Note: y is not in a data frame (table)

## --- Pearson's product-moment correlation --- 
##  
## Number of paired values with neither missing, n = 4000 
## Sample Correlation of x and y: r = 0.251 
##   
## Hypothesis Test of 0 Correlation:  t = 16.397,  df = 3998,  p-value = 0.000 
## 95% Confidence Interval for Correlation:  0.222 to 0.280 
## 

Another way to visualize a relationship when there are many data points is to bin the x-axis. Specify the number of bins with parameter n_bins. Plot() then computes the mean of y for each bin and connects the means by line segments. This procedure plots the conditional means by default without any assumption of form such as linearity. Specify the stat parameter for median to compute the median of y for each bin. The standard Plot() parameters fill, color, size and segments also apply.

Plot(x, y, n_bins=5)
## >>> Note: x is not in a data frame (table)
## >>> Note: y is not in a data frame (table)

## 
## Table: Summary Stats 
##  
##                x          y 
## -------  -------  --------- 
## n           4000       4000 
## n.miss         0          0 
## min       -3.239   -104.740 
## max        3.589    112.460 
## mean      -0.003      1.006 
## 
##  
## Table: mean of y for levels of x 
##  
##                   bin      n    midpt      mean 
## ---  ----------------  -----  -------  -------- 
## 1     [-3.246,-1.873]    116   -2.560   -16.734 
## 2     (-1.873,-0.508]   1090   -1.191    -5.699 
## 3      (-0.508,0.858]   2001    0.175     0.848 
## 4       (0.858,2.223]    743    1.541    12.374 
## 5       (2.223,3.596]     50    2.909    25.696

One Variable

The default plot for a single continuous variable includes not only the scatterplot, but also the superimposed violin plot and box plot, with outliers identified. Call this plot the VBS plot.

Plot(Salary)
## [Violin/Box/Scatterplot graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry

## --- Salary --- 
## Present: 37 
## Missing: 0 
## Total  : 37 
##  
## Mean         : 73795.557 
## Stnd Dev     : 21799.533 
## IQR          : 31012.560 
## Skew         : 0.190   [medcouple, -1 to 1] 
##  
## Minimum      : 46124.970 
## Lower Whisker: 46124.970 
## 1st Quartile : 56772.950 
## Median       : 69547.600 
## 3rd Quartile : 87785.510 
## Upper Whisker: 122563.380 
## Maximum      : 134419.230 
## 
##   
## --- Outliers ---     from the box plot: 1 
##  
## Small      Large 
## -----      ----- 
##             134419.23 
## 
## Number of duplicated values: 0 
## 
## Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.61      size of plotted points 
## out_size: 0.82  size of plotted outlier points 
## jitter_y: 0.45 random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points 
## bw: 9529.04       set bandwidth higher for smoother edges

Control the choice of the three superimposed plots – violin, box, and scatter – with the vbs_plot parameter. The default setting is "vbs" for all three plots. Here, for example, obtain just the box plot. Or, use the alias BoxPlot() in place of Plot().

Plot(Salary, vbs_plot="b")
## [Violin/Box/Scatterplot graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry

## --- Salary --- 
## Present: 37 
## Missing: 0 
## Total  : 37 
##  
## Mean         : 73795.557 
## Stnd Dev     : 21799.533 
## IQR          : 31012.560 
## Skew         : 0.190   [medcouple, -1 to 1] 
##  
## Minimum      : 46124.970 
## Lower Whisker: 46124.970 
## 1st Quartile : 56772.950 
## Median       : 69547.600 
## 3rd Quartile : 87785.510 
## Upper Whisker: 122563.380 
## Maximum      : 134419.230 
## 
##   
## --- Outliers ---     from the box plot: 1 
##  
## Small      Large 
## -----      ----- 
##             134419.23 
## 
## Number of duplicated values: 0

Do a frequency distribution by specifying the value of parameter stat_x, either "count" or if the y-axis is proportion, then "proportion" or "%". Can specify a custom bin width if desired with the parameter bin_width.

Plot(Salary, stat_x="%", bin_width=13000)
## >>> Suggestions
## Plot(Salary, stat_x="%", bin_width=13000, size=0)  # just line segments, no points 
## 
## --- Salary --- 
##  
##      n   miss         mean           sd          min          mdn          max 
##      37      0    73795.557    21799.533    46124.970    69547.600   134419.230 
## 
## 
## Bin Width: 13000 
## Number of Bins: 8 
##  
##              Bin  Midpnt  Count    Prop  Cumul.c  Cumul.p 
## --------------------------------------------------------- 
##   40000 >  53000   46500      5    0.14        5     0.14 
##   53000 >  66000   59500     10    0.27       15     0.41 
##   66000 >  79000   72500     10    0.27       25     0.68 
##   79000 >  92000   85500      4    0.11       29     0.78 
##   92000 > 105000   98500      4    0.11       33     0.89 
##  105000 > 118000  111500      2    0.05       35     0.95 
##  118000 > 131000  124500      1    0.03       36     0.97 
##  131000 > 144000  137500      1    0.03       37     1.00 
## 
## No (Box plot) outliers

Cleveland Dot Plot

Create a Cleveland dot plot when one of the variables has unique (ID) values. In this example, for a single variable, row names are on the y-axis. The default plots sorts by the value plotted with the default value of parameter sort_yx of "+" for an ascending plot. Set to "-" for a descending plot and "0" for no sorting.

Plot(Salary, row_names)

##  
## --- Salary --- 
##  
##      n   miss      mean        sd       min       mdn       max 
##      37      0   73795.6   21799.5   46125.0   69547.6  134419.2 
## 
##   
## --- Outliers ---     from the box plot: 1 
##  
## Small      Large 
## -----      ----- 
##             134419.2 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.80  size of plotted points 
## jitter_y: 0.00  random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points

The standard scatterplot version of a Cleveland dot plot follows, with no sorting and no line segments.

Plot(Salary, row_names, sort_yx="0", segments_y=FALSE)

##  
## --- Salary --- 
##  
##      n   miss      mean        sd       min       mdn       max 
##      37      0   73795.6   21799.5   46125.0   69547.6  134419.2 
## 
##   
## --- Outliers ---     from the box plot: 1 
##  
## Small      Large 
## -----      ----- 
##             134419.2 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.80  size of plotted points 
## jitter_y: 0.00  random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points

This Cleveland dot plot has two x-variables, indicated as a standard R vector with the c() function. In this situation, the two points on each row are connected with a line segment. By default the rows are sorted by distance between the successive points.

Plot(c(Pre, Post), row_names)

##  
## --- Pre --- 
##  
##      n   miss    mean      sd     min     mdn     max 
##      37      0    78.8    12.0    59.0    80.0   100.0 
##  
##  
## --- Post --- 
##  
##      n   miss    mean      sd     min     mdn     max 
##      37      0    81.0    11.6    59.0    84.0   100.0 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.80  size of plotted points 
## jitter_y: 0.00  random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points

Categorical and Continuous Variables

A mixture of categorical and continuous variables can be plotted a variety of ways, as illustrated below.

Two Continuous, One Categorical

Plot a scatterplot of two continuous variables for each level of a categorical variable on the same panel with the by parameter. Here, plot Years and Salary each for the two levels of Gender in the data. Colors and geometric plot shapes can distinguish between the plots. For all variables except an ordered factor, the default plots according to the default qualitative color palette, "hues", with the geometric shape of a point.

Plot(Years, Salary, by=Gender)

Change the plot colors with the fill (interior) and color (exterior or edge) parameters. Because there are two levels of the by variable, specify two fill colors and two edge colors each with an R vector defined by the c() function. Also, include the regression line for each group with the fit parameter and increase the size of the plotted points with the size parameter.

Plot(Years, Salary, by=Gender, size=2, fit="lm",
     fill=c("olivedrab3", "gold1"), 
     color=c("darkgreen", "gold4")
)

## 
## Gender: M   Line: b0 = 30842.335    b1 = 4047.307    Fit: MSE = 107,647,877   Rsq = 0.819
##  
## Gender: W   Line: b0 = 47109.787    b1 = 2882.272    Fit: MSE = 144,700,625   Rsq = 0.598
## 

Change the plotted shapes with the shape parameter. The default value is "circle" with both an exterior color and filled interior, specified with "color" and "fill". Other possible values, with fillable interiors, are "circle", "square", "diamond", "triup" (triangle up), and "tridown" (triangle down). Other possible values include all uppercase and lowercase letters, all digits, and most punctuation characters. The numbers 0 through 25 defined by the R points() function also apply. If plotting levels according to by, then list one shape for each level to be plotted.

Or, request default shapes across the different by groups by setting parameter shapes to "vary".

Plot(Years, Salary, by=Gender, shape="vary")

A Trellis (facet) plot creates a separate panel for the plot of each level of the categorical variable. Generate Trellis plots with the by1 parameter. In this example, plot the best-fit linear model for the data in each panel according to the fit parameter. By default, the 95% confidence interval for each line is also displayed.

Plot(Years, Salary, by1=Gender, fit="lm")
## [Trellis graphics from Deepayan Sarkar's lattice package]

## 
## Regression analysis of linearized Salary values
## Need back transformation of regression model to compute predicted values
## 
## Gender 1  Line: b0 = 30842.335  b1 = 4047.307   Fit: MSE = 107,647,877   Rsq = 0.819
## 
## Gender 2  Line: b0 = 47109.787  b1 = 2882.272   Fit: MSE = 144,700,625   Rsq = 0.598

Turn off the confidence interval by setting the parameter fit_se to 0 for the value of the confidence level.

One Continuous, One Categorical

A categorical variable plotted with a continuous variable results in a traditional scatterplot though, of course, the scatter is confined to the straight lines that represent the levels of the categorical variable, its values.

The first two parameters of Plot() are x and y. In this example, the categorical variable, Dept, listed second, specifies the y variable, as in y=Dept. There is no distinction in this function call for two continues variables or one continuous and one categorical. The Plot() function evaluates each variable for continuity and responds appropriately.

Plot(Salary, Dept)

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Dept: Department Employed 
##  
##        n   miss      mean        sd       min       mdn       max 
## ACCT    5      0   61792.8   12774.6   46125.0   69547.6   72502.5 
## ADMN    6      0   81277.1   27585.2   53788.3   71058.6  122563.4 
## FINC    4      0   69010.7   17852.5   57139.9   61937.6   95027.6 
## MKTG    6      0   70257.1   19869.8   51036.8   61659.0   99062.7 
## SALE   15      0   78830.1   23476.8   49189.0   77714.9  134419.2 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.80  size of plotted points 
## jitter_y: 0.00  random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points

To avoid point overlap, if there is at least one duplicated value of continuous y for any level of categorical x, by default some horizontal jitter for each plotted point is added, which was not needed in this example. Manually adjust the jitter with either parameter jitter_x or, if x is continuous and y categorical, the jitter_y parameter. In addition, if the categorical variable is an R factor or a variable of type character, by default the mean of the continuous variable is displayed at each level of the categorical variable, as well in the text output. If the categorical variable is numeric, better to convert the variable to a factor to have just the categories on the axis and not a continuous scale. For example, d$Gender <- factor(d$Gender).

Another helpful technique for large data sets is to add some fill transparency with the transparency parameter, with values such as 0.8 and 0.9. The combination of jitter and transparency allows for plotting many thousands of points.

An alternative display of the distribution of a continuous variable and a categorical variable is a superimposed violin, box, and scatter plot, a VBS plot. To plot the points in different colors according to the level of the categorical variable, invoke the by parameter. Here, plot Salary across the levels of Gender on the same panel.

Plot(Salary, by=Gender)
## [Violin/Box/Scatterplot graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry
## ttest(Salary ~ Gender)  # Add the data parameter if not the d data frame

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Gender 
##  
##      n   miss         mean           sd          min          mdn          max 
## M   18      0    81147.458    23128.436    49188.960    79792.950   134419.230 
## W   19      0    66830.598    18438.456    46124.970    61356.690   122563.380 
## 
##        Max Dupli- 
## Level   cations   Values 
## ------------------------------ 
## M           0 
## W           0 
## 
## Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.56      size of plotted points 
## out_size: 0.80  size of plotted outlier points 
## jitter_y: 0.54 random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points 
## bw: 9529.04       set bandwidth higher for smoother edges

Or, create a Trellis plot that consists of a VBS plot on a separate panel for each level of the categorical variable. Accomplish the Trellis plot with the by1 parameter. Here, plot Salary across the levels of Dept. Again, specify one, two, or, by default, all three superimposed plots: violin, box, and scatter. In this example, the categorical variable, Gender specifies the by1 variable.

Plot(Salary, by1=Gender)
## [Trellis graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry
## ttest(Salary ~ Gender)  # Add the data parameter if not the d data frame

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Gender: Man or Woman 
##  
##      n   miss         mean           sd          min          mdn          max 
## M   18      0    81147.458    23128.436    49188.960    79792.950   134419.230 
## W   19      0    66830.598    18438.456    46124.970    61356.690   122563.380 
## 
##        Max Dupli- 
## Level   cations   Values 
## ------------------------------ 
## M           0 
## W           0 
## 
## Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.56      size of plotted points 
## out_size: 0.80  size of plotted outlier points 
## jitter_y: 0.54 random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points 
## bw: 9529.04       set bandwidth higher for smoother edges

The default coloring of the boxes for variables other than an ordered factor follows the default qualitative palette, "hues". For an ordered factor, the fill color follows the default sequential palette of the corresponding theme, such as "blues". Customize colors with the box_fill parameter.

Just show the box plots according to the vbs_plot parameter, which has a default setting of vbs for the superimposed violin, box, and scatter plots. Set vbs_plot to "b". Or, use the alias BoxPlot(). Change the fill color of each box with the box_fill parameter. In addition to the traditional median for a box plot, show the mean as well as with the vbs_mean parameter. If specifying just one fill color, then all boxes are filled with that color.

Or, drop the box plot and only plot the violins and the scatter plots. Without the boxes, the violins take on the default colors. Specify a value of "vs" for the vbs_plot parameter. If only plotting the violins, then can also use the alias ViolinPlot(). Change the fill color of the violins with parameter violin_fill.

Plot(Salary, by1=Gender, vbs_plot="vs")
## [Trellis graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry
## ttest(Salary ~ Gender)  # Add the data parameter if not the d data frame

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Gender: Man or Woman 
##  
##      n   miss         mean           sd          min          mdn          max 
## M   18      0    81147.458    23128.436    49188.960    79792.950   134419.230 
## W   19      0    66830.598    18438.456    46124.970    61356.690   122563.380 
## 
##        Max Dupli- 
## Level   cations   Values 
## ------------------------------ 
## M           0 
## W           0 
## 
## Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.56      size of plotted points 
## out_size: 0.80  size of plotted outlier points 
## jitter_y: 0.54 random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points 
## bw: 9529.04       set bandwidth higher for smoother edges

The following plot uses the alias BoxPlot() to generate a Trellis plot of boxplots only across the levels of Gender.

BoxPlot(Salary, by1=Gender, vbs_mean=TRUE, box_fill="lightgoldenrod")
## [Trellis graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry
## ttest(Salary ~ Gender)  # Add the data parameter if not the d data frame

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Gender: Man or Woman 
##  
##      n   miss         mean           sd          min          mdn          max 
## M   18      0    81147.458    23128.436    49188.960    79792.950   134419.230 
## W   19      0    66830.598    18438.456    46124.970    61356.690   122563.380 
## 
##        Max Dupli- 
## Level   cations   Values 
## ------------------------------ 
## M           0 
## W           0

Show the different distributions of the continuous variable across the levels of the categorical variable with a scatterplot. Here, show the distribution of Salary for Males and Females across the various departments.

Plot(Salary, Dept, by=Gender)

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Dept: Department Employed 
##  
##        n   miss      mean        sd       min       mdn       max 
## ACCT    5      0   61792.8   12774.6   46125.0   69547.6   72502.5 
## ADMN    6      0   81277.1   27585.2   53788.3   71058.6  122563.4 
## FINC    4      0   69010.7   17852.5   57139.9   61937.6   95027.6 
## MKTG    6      0   70257.1   19869.8   51036.8   61659.0   99062.7 
## SALE   15      0   78830.1   23476.8   49189.0   77714.9  134419.2 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.80  size of plotted points 
## jitter_y: 0.00  random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points

One Continuous, Two Categorical

To do a Trellis plot with two categorical variables, invoke the by2 parameter in addition to the by1 parameter. By default, the box fill colors are unique for each level of the by1 variable, and then the colors cycle through all the values of the by2 variable. With so many panels to plot, explicitly set them in a single column by setting parameter n_col to 1. The corresponding row parameter is n_row.

Plot(Salary, by1=Gender, by2=Dept, n_col=1)
## [Trellis graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry
## ttest(Salary ~ Gender)  # Add the data parameter if not the d data frame

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Gender: Man or Woman 
##  
##      n   miss         mean           sd          min          mdn          max 
## M   18      0    81147.458    23128.436    49188.960    79792.950   134419.230 
## W   19      0    66830.598    18438.456    46124.970    61356.690   122563.380 
## 
##        Max Dupli- 
## Level   cations   Values 
## ------------------------------ 
## M           0 
## W           0 
## 
## Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.56      size of plotted points 
## out_size: 0.80  size of plotted outlier points 
## jitter_y: 0.54 random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points 
## bw: 9529.04       set bandwidth higher for smoother edges

To specify custom colors with the box_fill parameter, specify the number of colors according to the number of levels of the by1 variable. The colors for by1 then cycle over the by2 values.

Alternatively, invoke the by parameter and the by1 parameter. The values of the by variable plot as separate panels, the Trellis part, and the by variable plot for each panel.

Plot(Salary, by1=Dept, by=Gender, n_col=1)
## [Trellis graphics from Deepayan Sarkar's lattice package]
## 
## >>> Suggestions
## Plot(Salary, out_cut=2, fences=TRUE, vbs_mean=TRUE)  # Label two outliers ...
## Plot(Salary, box_adj=TRUE)  # Adjust boxplot whiskers for asymmetry
## ttest(Salary ~ Gender)  # Add the data parameter if not the d data frame
## ANOVA(Salary ~ Dept)  # Add the data parameter if not the d data frame

## Salary: Annual Salary (USD) 
##   - by levels of - 
## Gender: Department Employed 
##  
##        n   miss         mean           sd          min          mdn          max 
## ACCT    5      0    61792.776    12774.606    46124.970    69547.600    72502.500 
## ADMN    6      0    81277.117    27585.151    53788.260    71058.595   122563.380 
## FINC    4      0    69010.675    17852.498    57139.900    61937.625    95027.550 
## MKTG    6      0    70257.128    19869.812    51036.850    61658.990    99062.660 
## SALE   15      0    78830.065    23476.839    49188.960    77714.850   134419.230 
## 
##        Max Dupli- 
## Level   cations   Values 
## ------------------------------ 
## ACCT        0 
## ADMN        0 
## FINC        0 
## MKTG        0 
## SALE        0 
## 
## Parameter values (can be manually set) 
## ------------------------------------------------------- 
## size: 0.52      size of plotted points 
## out_size: 0.79  size of plotted outlier points 
## jitter_y: 0.50 random vertical movement of points 
## jitter_x: 0.00  random horizontal movement of points 
## bw: 9529.04       set bandwidth higher for smoother edges

Two Continuous, Three Categorical

Plot() can display the relationships for up to five variables. The two primary variables, x and y, that form the basis of the scatter plot, are continuous. Usually these two variables are listed first in the function call and so do not need their parameter names specified. Indicate two categorical variables that form the Trellis panels with parameters by1 and by2. Call these two variables the Trellis variables, which define a Trellis panel for each combination of their values. Finally, there can be a categorical grouping variable, the by variable, which plots different groups within each Trellis panel.

To illustrate, first, the data. Use the Cars93 data set that is installed with lessR, which describes characteristics of 1993 cars.

d <- Read("Cars93")
## 
## >>> Suggestions
## Recommended binary format for data files: feather
##   Create with Write(d, "your_file", format="feather")
## More details about your data, Enter:  details()  for d, or  details(name)
## 
## Data Types
## ------------------------------------------------------------
## character: Non-numeric data values
## integer: Numeric data values, integers only
## double: Numeric data values with decimal digits
## ------------------------------------------------------------
## 
##       Variable                  Missing  Unique 
##           Name     Type  Values  Values  Values   First and last values
## ------------------------------------------------------------------------------------------
##  1        Make character     93       0      32   Acura  Acura ... Volvo  Volvo
##  2        Type character     93       0       6   Small  Midsize ... Compact  Midsize
##  3    MinPrice    double     93       0      79   12.9  29.2  25.9 ... 22.9  21.8  24.8
##  4    MidPrice    double     93       0      81   15.9  33.9  29.1 ... 23.3  22.7  26.7
##  5    MaxPrice    double     93       0      79   18.8  38.7  32.3 ... 23.7  23.5  28.5
##  6     MPGcity   integer     93       0      21   25  18  20 ... 18  21  20
##  7    MPGhiway   integer     93       0      22   31  25  26 ... 25  28  28
##  8     Airbags   integer     93       0       3   0  2  1 ... 0  1  2
##  9  DriveTrain   integer     93       0       3   1  1  1 ... 1  0  1
## 10   Cylinders   integer     92       1       5   4  6  6 ... 6  4  5
## 11      Engine    double     93       0      26   1.8  3.2  2.8 ... 2.8  2.3  2.4
## 12          HP   integer     93       0      57   140  200  172 ... 178  114  168
## 13         RPM   integer     93       0      24   6300  5500  5500 ... 5800  5400  6200
## 14     RevMile   integer     93       0      78   2890  2335  2280 ... 2385  2215  2310
## 15      Manual   integer     93       0       2   1  1  1 ... 1  1  1
## 16     FuelCap    double     93       0      38   13.2  18  16.9 ... 18.5  15.8  19.3
## 17     PassCap   integer     93       0       6   5  5  5 ... 4  5  5
## 18      Length   integer     93       0      51   177  195  180 ... 159  190  184
## 19   Wheelbase   integer     93       0      27   102  115  102 ... 97  104  105
## 20       Width   integer     93       0      16   68  71  67 ... 66  67  69
## 21       Uturn   integer     93       0      14   37  38  37 ... 36  37  38
## 22    RearSeat    double     91       2      24   26.5  30  28 ... 26  29.5  30
## 23      LugCap   integer     82      11      16   11  15  14 ... 15  14  15
## 24      Weight   integer     93       0      81   2705  3560  3375 ... 2810  2985  3245
## 25      Source   integer     93       0       2   0  0  0 ... 0  0  0
## ------------------------------------------------------------------------------------------

The categorical variables are integer coded 0 and 1, so recode to R factors to obtain more descriptive labels.

d$Transmission <- factor(d$Manual, levels=0:1, labels=c("Auto", "Manual"))
d$Source <- factor(d$Source, levels=0:1, labels=c("Foreign", "Domestic"))

Plot MPGcity according to Weight. Specify the number of Cylinders and Manual transmission or not as Trellis conditioning variables to form the Trellis plot. Specify the Source of the vehicle, Foreign or Domestic as a grouping variable to plot with separate colors on each panel.

Plot(Weight, MPGcity, by1=Cylinders, by2=Transmission, by=Source, n_col=1)
## [Trellis graphics from Deepayan Sarkar's lattice package]

From the visualization the patterns emerge. As Weight increases city MPG decreases. Domestic cars tend to weigh more. Foreign cars tend to have fewer cylinders, which also leads to better fuel mileage.

Categorical Variables

To avoid over-plotting, the plot of two categorical variables results in a bubble plot of their joint frequencies.

d <- Read("Employee", quiet=TRUE)
Plot(Dept, Gender)

## Joint and Marginal Frequencies 
## ------------------------------ 
##  
##        Dept 
## Gender   ACCT ADMN FINC MKTG SALE Sum 
##   M         2    2    3    1   10  18 
##   W         3    4    1    5    5  18 
##   Sum       5    6    4    6   15  36 
## 
## Cramer's V: 0.415 
##  
## Chi-square Test of Independence:
##      Chisq = 6.200, df = 4, p-value = 0.185 
## >>> Low cell expected frequencies, chi-squared approximation may not be accurate 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## radius: 0.22    size of largest bubble 
## power: 0.50     relative bubble sizes

The parameter radius scales the size of the bubbles according to the size of the largest displayed bubble in inches. The power parameter sets the relative size of the bubbles. The default power value of 0.5 scales the bubbles so that the area of each bubble is the value of the corresponding sizing variable. A value of 1 scales so the radius of each bubble is the value of the sizing variable, increasing the discrepancy of size between the variables.

In this example, increase the absolute size of the bubbles as well as the relative discrepancy in their sizes. If the bubbles become too large, so that the largest bubbles become truncated, increase the spacing of the respective axes with the pad_x and/or pad_y parameters.

Plot(Dept, Gender, radius=.6, power=0.8, pad_x=0.05, pad_y=0.05)

## Joint and Marginal Frequencies 
## ------------------------------ 
##  
##        Dept 
## Gender   ACCT ADMN FINC MKTG SALE Sum 
##   M         2    2    3    1   10  18 
##   W         3    4    1    5    5  18 
##   Sum       5    6    4    6   15  36 
## 
## Cramer's V: 0.415 
##  
## Chi-square Test of Independence:
##      Chisq = 6.200, df = 4, p-value = 0.185 
## >>> Low cell expected frequencies, chi-squared approximation may not be accurate 
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## radius: 0.60    size of largest bubble 
## power: 0.80     relative bubble sizes

Alternatively, plot two categorical variables with a Trellis (facet) chart by invoking the by1 parameter. If the first listed variable in the function call, the x parameter, is categorical, the result is a dot chart for each level of the by1 variable.

Plot(Dept, by1=Gender)
## [Trellis graphics from Deepayan Sarkar's lattice package]

Plotting a single categorical variable yields the corresponding bubble plot of frequencies.

Plot(Dept)

## >>> Suggestions
## Plot(Dept, color_low="lemonchiffon2", color_hi="maroon3") 
## Plot(Dept, values="count")  # scatter plot of counts 
## 
## --- Dept --- 
## 
##                 ACCT   ADMN   FINC   MKTG   SALE    Total 
## Frequencies:       5      6      4      6     15       36 
## Proportions:   0.139  0.167  0.111  0.167  0.417    1.000 
## 
## Chi-squared test of null hypothesis of equal probabilities 
##   Chisq = 10.944, df = 4, p-value = 0.027
##  
##  
## 
## Some Parameter values (can be manually set) 
## ------------------------------------------------------- 
## radius: 0.22    size of largest bubble 
## power: 0.50     relative bubble sizes

Interactive Plots

An interactive visualization lets the user in real time change parameter values to change characteristics of the visualization. To create an interactive two-variable scatterplot of continuous variables with the employee data that displays the corresponding parameters, run the function interact() with "ScatterPlot" specified.

interact("ScatterPlot")

To create an interactive Trellis plot as a combined violin, box, and scatter plot with the five values of Dept from the Employee data set that displays the corresponding parameters, run the function interact() with "Trellis" specified.

interact("Trellis")

The functions are not run here because interactivity requires to run directly from the R console.

Full Manual

Use the base R help() function to view the full manual for Plot(). Simply enter a question mark followed by the name of the function.

?Plot

More

More on Scatterplots, Time Series plots, and other visualizations from lessR and other packages such as ggplot2 at:

Gerbing, D., R Visualizations: Derive Meaning from Data, CRC Press, May, 2020, ISBN 978-1138599635.