Stacked plots and Facet grids

Stacked plots and Facet grids#

Summary

On this page, you will see how to

  • use .plot.facet_grid.line and .plot.facet_grid.errorbands to stack multiple lines in a single plot, using hue to differentiate them.

  • plot multiple panels in a single image, using the hue, row, and col keys.

  • use .plot.facet_grid.with_auto_encoding to automatically distribute variables onto available plot dimensions.

  • use col_wrap: auto to automatically make the plot more square.

Complete example: Stacked Errorbands

stacked_errorbands:
  based_on:
    - .creator.multiverse
    - .plot.facet_grid.errorbands

  # Select the infected population
  select_and_combine:
    fields:
      infected:
        path: densities
        transform:
          - .sel: [!dag_prev , { kind: infected }]
    subspace:
      immunity rate: [ 0.3 ]

  # Calculate mean and std for each 'transmission rate' value
  transform:
    - .mean: [!dag_tag infected]
      kwargs:
        dim: seed
      tag: mean
    - .std: [!dag_tag infected]
      kwargs:
        dim: seed
      tag: std
    - xr.Dataset:
      - infected density: !dag_tag mean
        err: !dag_tag std
      tag: data

  # Distribute the variables accordingly
  x: time
  y: infected density
  yerr: err
  hue: transmission rate

  # Set the helpers
  helpers:
    set_labels:
      y: Density [1/A]
    set_title:
      title: Density of agent kinds

  # Use some pretty colors and latex
  style:
    text.usetex: True
    mathtext.fontset: stix
    font.family: serif
    axes.prop_cycle: cycler('color', ['#AFD8BC', '#FFCC66', '#006666' ])

Complete example: Facet grid

panel_errorbands:
  based_on:
    - .creator.multiverse
    - .plot.facet_grid.errorbands

  # Select the infected agents
  # (three sweep dimensions: immunity rate, transmission rate, seed)
  select_and_combine:
    fields:
      infected:
        path: densities
        transform:
          - .sel: [!dag_prev , { kind: infected }]

  # Calculate mean and std for each
  transform:
    - .mean: [!dag_tag infected, seed]
      tag: mean
    - .std: [!dag_tag infected, seed]
      tag: std
    - xr.Dataset:
      - infected density: !dag_tag mean
        err: !dag_tag std
      tag: data

  # Distribute the variables
  x: time
  y: infected density
  yerr: err
  row: transmission rate
  col: immunity rate

  # Set the same limits for all (makes it easier to compare the panels)
  helpers:
    set_limits:
      y: [ 0, 0.2 ]

  # Use some pretty colors and latex
  color: '#CC3333'
  style:
    text.usetex: True
    mathtext.fontset: stix
    font.family: serif

In the previous section we plotted a single line; now let’s see how to plot multiple lines with legends, all in the same plot. Using our SEIRD model, let’s look at how the susceptible, infected, and recovered populations evolve together:

densities:
  based_on:
    - .creator.universe
    - .plot.facet_grid.line

  select:
    data:
      path: data/SEIRD/densities
      transform:
        - .sel: [!dag_prev , { kind: [susceptible, infected, recovered] }]

  x: time

Now that we’ve added more than one y-value, we need to tell the line-plot what to put on the x-axis (x: time). Instead of specifying the x-value, we could also tell it what the color represents – the two are equivalent. To do this, simply replace the following line:

# x: time
hue: kind

In both cases, we get something like this:

Stacked SEIRD universe plot

We used LaTeX and some pretty colours to spruce everything up – see Customising plot styles for more details.

Stacked line plot with one sweep dimension#

Let’s compare the infection curves for three different values of the transmission rate p_transmit of the virus.

infection_curves:
  based_on:
    - .creator.multiverse
    - .plot.facet_grid.line

  select_and_combine:
    fields:
      data:
        path: data/SEIRD/densities
        transform:
          - .sel: [!dag_prev , { kind: [infected] }]

  x: time

Since this is a multiverse plot, we must use the corresponding creator, and use the select_and_combine key to gather the data. In this example, transform block only adds a data tag to the data, without performing any actual transformation operations.

Note

For facet_grid() plots, the data tag must always be defined, even when not applying any sort of transformation; that tag is where the plot expects to find the data to plot. Here, we are defining the data tag in the select step. Other plot functions may have different requirements.

This produces the following output:

Stacked density plot

Unsurprisingly, we see the peak of infection increasing as the virus becomes more transmissible.

Stacked line plot with one sweep dimension and statistics#

Let’s do the same thing, but with each infection curve representing an average over a few simulation runs with different initial seeds. This assumes that we have performed a two-dimensional multiverse run, sweeping over both the seed and the transmission rate p_transmit. The only thing we need to change from the previous entry is the transform block:

transform:
  - .mean: [!dag_tag infected, seed]
    tag: data
Stacked density plot with average over seed dimension

This would be much more meaningful if we could add errorbands to each of the curves, so let’s do that:

infection_curves_averaged:

  # Use the errorbands function!
  based_on:
    - .creator.multiverse
    - .plot.facet_grid.errorbands

  # This is the same as above
  select_and_combine:
    fields:
      infected:
        path: densities
        transform:
          - .sel: [!dag_prev , { kind: [infected] }]

  # Calculate mean and standard deviation along the 'seed' dimension
  transform:
    - .mean: [!dag_tag infected, seed]
      tag: mean
    - .std: [!dag_tag infected, seed]
      tag: std
    - xr.Dataset:
      - infected density: !dag_tag mean
        err: !dag_tag std
      tag: data

  x: time
  y: infected density
  yerr: err
  hue: transmission rate

Because the data is two-dimensional, we need to tell the plot function what to put on the x-axis, and what to stack: that’s why need both the hue and x keys. Make sure to adjust the hue key to whatever you named your sweep dimension!

Errorbands plot with hue dimension

Trying to debug errors in your DAG?

Have a look at Debugging DAG computations for approaches to do that.

Facet grids#

The stacked line plots we have just discussed are examples of facet grids. Facet grids are a simple way of visualising the results of parameter sweeps in a single image, either by showing several plots in a single frame, or by combining several frames into single image. Showing several panels in a single image can be useful when there are simply too many variables for a single plot, or when plotting everything on a single would clutter the plot. In such situations, you may wish to produce something like this:

A facet grid example

Here, we are showing the output of a 3-dimensional parameter sweep: we are sweeping over the transmission rate, over the immunity rate, and over the initial seed. Each panel shows the density of infected agents over time (x-axis), with the transmission rate on the rows, and the immunity rate on the columns. Within each panel, we are averaging over the seed and producing an errorband plot, using the .plots.facet_grid.errorbands function.

Generating this plot is a simple modification away from our previous configuration; all we need to do is to divide up our variables amongst the rows and columns, using the row and col keys:

infection_curves_averaged:

  # Same as above
  based_on:
    - .creator.multiverse
    - .plot.facet_grid.errorbands

  select_and_combine:
  # also same as above...

  transform:
  # same as above ...

  x: time
  y: infected density
  yerr: err
  row: transmission rate
  col: immunity rate

  color: crimson
  helpers:
    set_limits:
       y: [0, 0.2]

The transformation framework takes care of everything else. Notice that we have set the y-limits to all be equal, so that we can compare the curves at a single glance.

The facet_grid() plot allows us to simultaneously plot parameters onto rows, columns, the y-axis, and also make use of the hue; let’s additionally include the susceptible and recovered agents in our plots:

A facet grid example

A little crowded perhaps, but we get the idea. All this requires is to include the other two kinds in our selection, and to set the hue key:

infection_curves_averaged:

  based_on:
    - # Same as above

  # Also select the other kinds:
  select_and_combine:
    fields:
      infected:
        path: densities
        transform:
      - .sel: [!dag_prev , { kind: [susceptible, infected, recovered] }]

  transform:
    - # same as above ...

  x: time
  y: infected density
  yerr: err
  row: transmission rate
  col: immunity rate
  hue: kind

  helpers:
    set_limits:
       y: [0, 0.6]

Note that the legend and row and column titles are automatically plotted.

Hint

You may sometimes not want to plot all values of a parameter; for example, for the plot above, we may just be interested in immunity rate = 0, 0.1, 0.2, and transmission rate = 0.2, 0.4. This is easily achieved using subspace selection.

Hint

If you have lots of columns and few rows, use col_wrap: auto together with .plot.facet_grid.with_auto_encoding (see below) to create a more square plot.

Auto-encoding#

If you don’t care which variables go where, you can include the .plot.facet_grid.with_auto_encoding modifier into your plot:

based_on:
  # ...
  - .plot.facet_grid.with_auto_encoding
  # ...

This will automatically distribute the variables onto any available dimensions. Variables will be distributed in a certain order, see the determine_encoding() dantro function.

Hint

Automatically determining the encoding can be useful if you want to implement more generic plots that do not depend so much on the dimensionality of your multiverse simulation run. They are best suited for getting an overview of your simulation results.

However, if you want to be sure that a specific variable is represented in a certain way, it’s best to specify the encoding (x, col, …) explicitly. For publication-ready figures, this explicit definition is more suited.

To further control in which order dimensions are populated, you can pass a dict to the auto_encoding argument (instead of a boolean):

based_on:
  # ...
  - .plot.facet_grid.line
  - .plot.facet_grid.with_auto_encoding
  # ...

# change the order in which encodings are populated
auto_encoding:
  line: [x, col, hue, frames, row]  # default: [x, hue, col, row, frames]

Hint

The .plot.facet_grid.with_auto_encoding base config also sets the col_wrap: auto argument, which aims to make facet grid plots with many subplots more square by wrapping after sqrt(num_cols). This is ignored if the row encoding is specified.

Hint

The expected_multiverse_ndim entry in a multiverse plot configuration can be used to skip a plot for unsupported dimensionalities:

my_multiverse_plot:
  # ...

  # Only plot if the multiverse is 1-, 2-, or 3-dimensional
  expected_multiverse_ndim: [1, 2, 3]

Alternatively, you can also use the .skip base plot configs, which define a bunch of these ready-to-use; see Base Plot Configuration Pool.