figures with matplotlib

By Jochen Voss, on 2009-02-03

I like to use the matplotlib Python library to create figures for use in my articles. Unfortunately, the matplotlib default settings seem to be optimised for screen-viewing, so creating pictures for inclusion in a scientific paper needs some fiddling. Here is an example script which sets up things for such a figure.

#! /usr/bin/env python

import matplotlib
matplotlib.use("PS")
from pylab import *

rc("font", family="serif")
rc("font", size=10)

width = 4.5
height = 1.4
rc("figure.subplot", left=(22/72.27)/width)
rc("figure.subplot", right=(width-10/72.27)/width)
rc("figure.subplot", bottom=(14/72.27)/height)
rc("figure.subplot", top=(height-7/72.27)/height)
figure(figsize=(width, height))

x = loadtxt("x.dat")
plot(x[:,0], x[:,1], "k-")

savefig("figure.eps")

The script performs the following steps:

The matplotlib.use statement tells matplotlib to use one of the non-interactive backends. Without this statement, the script would need a connections to an X-windows server to run.
The two rc statement set the font family and size for the labels on the axes to match the font used in the article's text (matplotlib uses a 12pt sans-serif font by default).
The rc("figure.subplot", ...) settings and the figsize argument to the figure call set the image geometry. Since the text on journal pages typically is about 5in wide, a total figure width of 4.5in is often a good value. The margins set by the rc statements have to be given as fractions of the image width/height and must be big enough to contain the axis labels. A bit of experimentation helps to find good values; here we use a 14pt margin at the bottom (10pt font height plus some space), 22pt left margin (depends on the number of digits in the y-axis labels), 7pt for the top margin (space for half of the top-most y-axis label, and then some more) and 10pt to the right (enough space for half the right-most x-axis label).
The color code "k" in the plot command sets the plot color to black. Matplotlib default is blue, but some journals charge you for use of colour in your articles (and also it is nice if you can print things on a b/w printer).
The savefig command creates an encapsulated PostScript file. This format is good for inclusion in TeX documents. The file can be converted to PDF using the epstopdf command as needed.