Friday 15 November 2019

My Matplotlib Cheatsheet (#1)

I find myself Googling the same matplotlib/pyplot queries over and over again. To make life easy, I started collecting some of them in a series of blog posts.
In this first post, I'll look at subplots and annotations.

Turn off axes


We can remove axes, ticks, borders, etc. with ax.axis('off'). This can be used to remove unnecessary subplots created with the subplots function from pyplot, for instance, when we only want to use the upper triangle of the grid. Here's an example:


The result is:


Share axes between subplots after plotting


An alternative way of making a ragged array of subplots makes use of gridspec. The problem here is that it is a bit more difficult to share x and y axes. Of course add_subplot has keyword arguments sharex and sharey, but then we have to distinguish between the first and subsequent subplots. A better solution is the get_shared_x_axes() method. Here's an example:


The result is:

Hybrid (or blended) transforms for annotations


When you annotate a point in a plot, the location of the text is often relative to the data in one coordinate, but relative to the axis (e.g. in the middle) in the other. I used to do this with inverse transforms, but it turns out that there is a better way: the blended_transform_factory function from matplotlib.transforms.
Suppose that I want to annotate three points in three subplots. The arrows should point to these three points, and I want the text to be located above the point, but the text in the 3 subplots has to be vertically aligned.



Notice that the y-axes are not shared between the subplots! To accomplish the alignment, we have to use the annotate method with a custom transform.

Monday 11 November 2019

Using constant Stan functions for parameter array indices in ODE models


Stan's ODE solver has a fixed signature. The state, parameters and data has to be given as arrays. This can get confusing during development of a model, since parameters can change to constants (i.e. data), the number of parameters can change and even the state variables could change. Errors can easily creep in since the user has to correctly change all indices in the ODE function, and in (e.g.) the model block. A nice way to solve this is using constant functions. Constants in Stan are functions without an argument that return the constant value. For instance pi() returns 3.14159265... The user can define such constants in the functions block. Suppose that we want to fit the Lotka-Volterra model to data. The system of ODEs is given by \[ \frac{dx}{dt} = ax - bxy\,,\quad \frac{dy}{dt} = cbxy - dy \] and so we have a 2-dimenional state, and we need a parameter vector of length 4. In the function block, we will define a function int idx_a() { return 1; } that returns the index of the parameter \(a\) in the parameter vector, and we define similar functions for the other parameters. The full model can be implemented in Stan as shown below. The data Preys and Predators is assumed to be Poisson-distributed with mean \(Kx\) and \(Ky\), respectively, for some large constant \(K\). I fitted the model to some randomly generated data, which resulted in figure above.


Of course, this is still a low-dimensional model with a small number of parameters, but I found that even in a simple model, defining parameter indices in this way keeps everything concise.
I used the following Python script to generate the data and interface with Stan.


The following Figure show the parameter estimates together with the "real" parameter values