add utility method to plot the pdf of a variable

[drbenvincent]

In discussions in PyMC Labs, a client asked if there was a simple utility function to plot the pdf of a PyMC variable.

As a quick hack I came up with the following:

Continuous

def plot_cont(self):
    """Plot pdf of continuous dist, with semi clever setting of range"""
    samples = self.random(size=10_000)
    x = np.linspace(np.min(samples), np.max(samples), 1000)
    plt.plot(x, np.exp(self.logp(x)).eval())

# add plot method to abstract class Continuous
pm.Continuous.plot = plot_cont

# example use
pm.Normal.dist(mu=1, sd=2).plot()
pm.Laplace.dist(mu=0, b=1).plot()

which results in the following

Discrete

def plot_disc(self):
    """Plot pdf of discrete dist, with semi clever setting of range"""
    samples = self.random(size=10_000)
    x = np.arange(np.min(samples), np.max(samples)+1)
    plt.plot(x, np.exp(self.logp(x)).eval(), "-o")

# add plot method to abstract class Continuous
pm.Discrete.plot = plot_disc

# example use
pm.Binomial.dist(n=10, p=0.2).plot()
pm.Geometric.dist(p=0.5).plot()

which results in this

So this issue is to see what people think about adding this functionality.

I've contributed example notebooks, but not to core PyMC code before, so it may be naive but... Maybe some more polished version could be added as methods of pm.Continuous and pm.Discrete?

Thoughts and feedback welcome.

[michaelosthege]

In the past I used np.exp(pm. Normal().logp(x).eval()) but that API is now a hard-to-find functional API of pm.logp.

The bigger question though is what to do with multidimensional RVs?

[drbenvincent]

The bigger question though is what to do with multidimensional RVs?

In the first instance I think it makes sense to implement for univariate distributions. And override the method in distributions which are inherently multidimensional, potentially with a not implemented exception.

At a later stage you could implement custom plot functions for bivariate distributions, for example.

[michaelosthege]

If you're looking for a place to put such a plotting function, that'd probably be pm.plots.

[bwengals]

Can't help but chime in and +1 this, I at least make plots like these just about every single time I use pymc3. Though I call plt.hist on samples and then fiddle with the x limits, so this is much better. I also think it would be extra nice if arviz could be leveraged for visual continuity if possible.

[aloctavodia]

Somewhat related, in Bambi we have a method to plot prior samples. https://bambinos.github.io/bambi/main/api_reference.html#bambi.models.Model.plot_priors

[drbenvincent]

I also think it would be extra nice if arviz could be leveraged for visual continuity if possible.

I'm assuming we don't want to PyMC dependent upon arviz? In which case we'd have to just emulate the style? But it would be presumably be pretty easy by optionally doing

import arviz as az
az.style.use("arviz-darkgrid")

Overall I think we could make this pretty minimal. Users may want to compose their own complex and possibly multi-panel plots.

[michaelosthege]

We have a dependency on ArviZ and since ArviZ no longer depends on PyMC that's fine.

But IMO any change of default style is something the user needs to do. I for example don't like the "arviz-darkgrid" style 😱

[drbenvincent]

But IMO any change of default style is something the user needs to do. I for example don't like the "arviz-darkgrid" style 😱

I agree. I prefer simpler styles more suitable for publication for example

[ferrine]

I like that proposal. We can raise an error on multidimensional variables. Additionally, a more flexible API is needed here. As any plotting function in the plt namespace, this should take optional axes as input and output the used axes

[drbenvincent]

Yes. Was planning on full axes luxury

[ricardoV94]

This should probably not me a method, because we don't really have class instances in V4 anymore, but something that accepts a RV.

rv1 = pm.Normal.dist(0, 1)
with pm.Model() as m:
    rv2 = pm.Normal("rv2", 0, 1)

pm.plot(rv1)
pm.plot(rv2)

Both would yield the same. This has the advantage that you can plot the variables you defined in the model without having to rewrite with the .dist API

In V4, rv1 and rv2 are identical for this purpose.

[lancechua]

Hi, wanted to add to this since I'd find this feature quite useful as well.
The approach I took was to determine the plot domain based on the inverse cdf.
This has the advantage of not needing to sample, but does require implementing the quantile function.
I'd say it's decent by default but needs tweaking for longer tailed and positive only distributions.

Here's a colab demo notebook for proof of concept.
https://colab.research.google.com/drive/1yLczeGk09eeEnrlUoaJ57yQKJgCnPNdg

[aloctavodia]

To help interpret the pdf we can complement it with statistics such as the mean, HDI and/or quantiles. For example in this picture the dot is the mean, the thick line the IQR and the think line the 94% HDI, this is similar as the information presented in a forestplot.