Visualization with Matplotlib

Matplotlib is a popular graphing package for python and works smoothly with myokit.

Matplotlib has its own documentation. For convenience, the most important commands are listed here:

figure()

Creates a new figure

subplot(321)

Indicates the next figure will be 1st part of a subplot containing 3 rows and 2 columns. An alternative syntax is subplot(3,2,1). (docs)

plot(x,y)

Creates a plot of y versus x

The type of marker can be set with the third positional argument:

plot(x, y, '*')

Label, color and line width can be set with:

plot(x, y, label='y versus x', color='blue', lw=3)

show()

Displays the created plots

figure.savefig(filename)

Saves a figure to a file. (docs)

title(text)

Sets a title

suptitle(t)

Adds a title above the normal title

axis([xmin, xmax, ymin, ymax])

Sets the limits for the currents axes. Make sure to use axis with an ‘i’! The axes command creates a new subplot.

Run without arguments to obtain to current axis.

xlim(min, max), ylim(min, max)

Limits can be set individually with xlim() and ylim(). Call without arguments to obtain the current limits.

legend()

Using plot(x,y,label=’abc’) you can create labelled plots. The legend() commands will use these to build a legend.

The legend’s location can be set with the loc keyword and string values such as “upper right”, “left”, “lower” or “center”. To create multi-column legends, use the keyword ncol, for example ncol=2.

grid()

Toggles the grid ub the current subplot. Use True or False to set the state of the grid explicitly.

figtext(x, y, s)

Add text s at coordinates x and y (both in range [0..1])

text(x, y, s)

Add text at plotted coordinates x and y

loglog(x,y)

Using loglog, semilogx or semilogy instead of plot() you can create plots on logarithmic axes.

quiver(x,y,u,v)

Creates vector plots:

x = linspace(0,10,11)
y = linspace(0,15,16)
(X,Y) = meshgrid(x,y)
u = 5*X
v = 5*Y
quiver(X,Y,u,v,angles='xy',scale=1000,color='r')

xlabel(s), ylabel(s)

Add or set label on x or y axis

Customizing the axes

To further customize the axis, use the axes object returned by the subplot

Example

The following is an example plot script for running in the GUI:

[[script]]
import myokit
import matplotlib.pyplot as plt

# Get model & protocol from magic methods
m = get_model()
p = get_protocol()

# Create simulation
s = myokit.Simulation(m, p)

# Run simulation
d = s.run(1000)

# Display the result
t = d['environment.t']
v = d['membrane.V']
plt.plot(t, v)
plt.grid(True)
plt.title('Membrane potential versus time')
plt.show()