Support violin plot and probability density plots

[kanitw]

From https://vega.github.io/vega/examples/violin-plot/

A violin plot visualizes a distribution of quantitative values as a continuous approximation of the probability density function, computed using kernel density estimation (KDE). The densities are additionally annotated with the median value and interquartile range, shown as black lines. Violin plots can be more informative than classical box plots.

https://vega.github.io/vega/examples/probability-density/ is another related example

• Understand https://vega.github.io/vega/examples/violin-plot/ and https://vega.github.io/vega/examples/probability-density/ examples throughly, search online to understand other violin and density plot variants, and define the scope that we want to support.

• Understand how we implement composite mark thoroughly by looking at the [box-plot codebase](https://github.com/vega/vega-lite/blob/master/src/compositemark/boxplot.ts. (By summer, we should have reasonable error-bar example as well.)

• Design density transform in Vega-Lite and see if we can already use area mark to reproduce the density area for violin.

• Design composite mark syntax for violin (and density plot?)

  • First we can focus on just the violin area part: design MarkDefinition block for Violin so that we can define property of the underlying density transform and other related properties
  • Decide if we need a composite mark for density plot -- (probably yes), and make sure that the syntax for violin and density are consistent. (Also think if there is a better name for density too)
  • For violin plot, we need to decide if we want to include interquartile range and median as a part of the violin composite mark (which is sort of like the "box" overlay on top of violin plot). The syntax here should be very consistent with box-plot.

• Implement the code. Note that there is probably a good way to share at least some part of the implementation between the violin and density plot.

[kanitw]

The tricky part about this is that Vega's Violin plot depends on the Vega facet operator to split data into subgroups between passing it to density transform. (Density happens inside nested facet.)

1. Consider the solution above that suggests implementing density transform first.
   Given VL's facet also always applies layout, we can't reproduce the violin example with axis using implement density as a transform unless we do one of the following:

a) Make Vega density supports groupby (which is basically in place faceting)
b) Support a variant of facet without layout (pure facet in the data transformation sense)

Note: we can reproduce violin plot using VL facet operator, but we will then rely on row instead of y position for each violin.

2. Alternatively, we could consider implementing violin as its own special mark that produce underlying density transform. However, this approach will be less composable. (For example, density plots https://vega.github.io/vega/examples/probability-density/ shouldn't be its own mark but rather using area plotting output from density transforms.)

[kanitw]

We meet today to talk about this and conclude that we should make Vega density transform supports groupby.

[HarvsG]

We meet today to talk about this and conclude that we should make Vega density transform supports groupby.

@kanitw Any progress on implementation?

[kanitw]

No update yet

[romainmartinez]

Thanks for Vega-lite.

I often use violin plots and I am looking forward to use them in Vega-lite/Altair.

In addition, I use a lot of ridge plots (half violin) like this one:

Would you consider adding an option to the violin plot to allow similar figures to be made?

I made an implementation in python, with mark area and a custom kde function, but it is rather tedious.

Also, would similar figures in histogram be possible (for discrete variable)?

I'm sure anyone using Bayesian statistics would be grateful.

[domoritz]

Yes, once we have a kde transform in Vega, we can also support ridge plots.

[denisshepelin]

Yes, once we have a kde transform in Vega, we can also support ridge plots.

Has it already landed in the vega 5.0 (https://vega.github.io/vega/docs/transforms/density/)?