Trellis Plots with lessR

## The VBS Plot

The VBS plot is a superimposition of three plots: a violin plot, a box plot, and a 1D scatterplot. Its purpose is to visualize the distribution of a continuous variable. Unlike its primary competitor, the more traditional histogram, the VBS plot does not require binning of the values of the variable.

For a general presentation of using `R` and `lessR`, select one or both of the following sources.

- online book chapter, which contains nothing specific about VBS plots but does provide a general introduction to doing `R` data analysis
- within a working `R` session, enter `browseVignettes("lessR")`, then select the `Scatter, Box, and Violin Plots` vignette
- within a working `R` session, enter `?Plot` to access the manual that describes the `Plot()` function

### Box Plot

The box in a box plot of a continuous variable is based on the interquartile range or IQR, the positive difference between what is essentially the first and third quartiles, the range of data that contains the middle 50% of all the data values. The box’s width is the IQR, with a line through the median and perpendicular lines called whiskers extending out from the edges. The whiskers extend to the to respective small value and largest value that are not outliers, values considerable different from most remaining values of a distribution.

### Violin Plot

The violin plot is an updated version of the boxplot that replaces the box with a density plot, a smoothed histogram, and its mirror image. The violin plot transforms the straight edges of the box into information that shows the concentration of data values along the horizontal axis. The general appearance of a density plot and its mirror image may sometimes resemble a violin, hence the name.

### 1D Scatterplot

The one-variable scatterplot plots a point for every data value along the same axis.

### Palettes Addressed to Color-Blindness

Typical color palettes are not designed to account for color-blindness. Two palettes included in `lessR` do permit more sensitivity to differentiate among objects with various types of color blindness: `Okabe-Ito` and `viridis`. These are qualitative palettes, which means that the hue varies across the plotted objects. Specify these, or other palettes, as the value for the `fill` parameter, available both by entering a function call in the R console or via the interactive analysis.

### Parameters

For the full list of `Plot()` parameters, see the manual obtained by entering `?Plot`. These listed parameters are those provided in the interactive session from `interact("Trellis")`.

#### `x`-variable

  The numerical variable from which to construct the VBS plot.

#### `by1`-variable

  Optional categorical variable to create a Trellis for each level of the variable.

#### Points

fill
  interior color of a bar
color
  exterior color of a bar, i.e., its border
transparency
  transparency level of `0` (none) to `1` (completely transparent)
size
  size of the plotted points
shape
  shape of the plotted points

#### Objects

vbs_plot
  A character string that specifies the components of the integrated Violin-Box-Scatterplot (VBS) of a continuous variable. A `"v"` in the string indicates a violin plot, a `"b"` indicates a box plot with flagged outliers, and a `"s"` indicates a 1-variable scatterplot. Default value is `"vbs"`. The characters can be in any order and upper- or lower-case.
violin_fill
  interior color of each violin in a violin plot
box_fill
  interior color of each box in a box plot

#### Jitter

jitter_y
  jitter applied to the `y`-variable coordinates

#### Save

width
  width of saved pdf file, in inches
height
  height of saved pdf file, in inches