Scientific quality figures

1) Using SciencePlots

SciencePlots is a Python pakage that provides Matplotlib styles for scientific figures. Install with:

$ pip install SciencePlots

To use, simple add the import and select the style:

import matplotlib.pyplot as plt
import scienceplots

plt.style.use('science')

To use any of the styles temporarily, you can use a constext manager:

with plt.style.context('science'):
    plt.figure()
    plt.plot(x, y)
    plt.show()

More information and available styles can be found here.

2) Using a predifined stylesheet

You can create and install a custom Matplotlib style. Install the styles by copying the respective *.mplstyle file into your Matplotlib style directory. To check where this is, in an interactive python console type:

import matplotlib
print(matplotlib.get_configdir())

You should get back something like /home/johndoe/.matplotlib. You can then put the *.mplstyle file in /home/johndoe/.matplotlib/stylelib/ (you may need to create the stylelib directory). Here is a base configuration for a scientific style:

# Matplotlib style for scientific plotting
# Base style

# Set color cycle: blue, green, yellow, red, violet, gray
axes.prop_cycle : cycler('color', ['0C5DA5', '00B945', 'FF9500', 'FF2C00', '845B97', '474747', '9e9e9e'])

# Set default figure size
figure.figsize : 3.5, 2.625

# Set x axis
xtick.direction : in
xtick.major.size : 3
xtick.major.width : 0.5
xtick.minor.size : 1.5
xtick.minor.width : 0.5
xtick.minor.visible : True
#xtick.top : True

# Set y axis
ytick.direction : in
ytick.major.size : 3
ytick.major.width : 0.5
ytick.minor.size : 1.5
ytick.minor.width : 0.5
ytick.minor.visible : True
#ytick.right : True

# Set line widths
axes.linewidth : 0.5
grid.linewidth : 0.5
lines.linewidth : 1.

# Remove legend frame
legend.frameon : False

# Always save as 'tight'
savefig.bbox : tight
savefig.pad_inches : 0.05

# Use serif fonts
font.serif : cmr10, Computer Modern Serif, DejaVu Serif
font.family : serif
axes.formatter.use_mathtext : True
mathtext.fontset : cm

# Use LaTeX for math formatting
text.usetex : True
text.latex.preamble : \usepackage{amsmath} \usepackage{amssymb}

You can then use the styles in a similar fashion to that shown above. The following will apply the style globally:

plt.style.use('science')

You can also combine multiple styles by:

plt.style.use(['science', 'grid'])

To use styles on a figure by figure basis, use a contect manager:

with plt.style.context('science'):
    plt.figure()
    plt.plot(x, y)
    plt.show()

More styles here.

3) Additional usefull formating

import matplotlib.pyplot as plt
from matplotlib.offsetbox import AnchoredText

with plt.style.context('science'):
    fig, ax = plt.subplots()

    ax = plot(x, y)

    # Labels
    ax.set_xlabel(r'$D_{12}$ $\mathrm{(cm^2 s^{-1})}$')  # x-axis label using LaTeX
    ax.set_ylabel(r'Y axis label')  # y-axis label using LaTeX

    # Ticks and grids
    ax.grid(False)  # Remove grid
    ax.set_xlim([1, 11])  # Set x-axis limits
    ax.set_ylim([6.5, 8.5])  # Set y-axis limits

    ax.ticklabel_format(style='sci', axis='x', scilimits=(0,0))  # Set x-axis ticks to scientific notation
    ax.ticklabel_format(style='sci', axis='both', scilimits=(0,0))  # Set both axis ticks to scientific notation

    # Add a text box to a corner of the graph with e.g. 'a)'
    anchor_text = AnchoredText('a)', pad=0, loc='upper right', frameon=False, prop=dict(fontweight="bold", fontsize=12, fontfamily='serif'))
    ax.add_artist(anchor_text)

    plt.tight_layout()

    fig.set_size_inches(5.25, 3.95)  # Set figure size in inches

    fig.savefig('fig1.png', dpi=300, bbox_inches='tight')  # Save figure in png
    fig.savefig('fig1.pdf', dpi=300, bbox_inches='tight')  # Save figure in pdf

Sizing images correctly

If a journal's style guide tells the widths of the columns, you can use those values when generating your figure. If it doesn't tell the width, you can use the printlen LaTeX package to print it out inside your document:

...
% In the preamble
\usepackage{printlen}
...
% In a figure environment
  \begin{center}
    \includegraphics[width=\columnwidth]{example_fig}
  \end{center}
  \caption{%
    \label{fig:example_fig}
    In this figure caption, I can see that the width of
    one column is \printlength{\columnwidth}.}
...

Once we find the correct width, we use it in our python script:

pt = 1./72.27  # 72.27 points to an inch

jour_sizes = {
    "PRD": {"onecol": 246*pt, "twocol": 510*pt},
    "CQG": {"onecol": 374*pt},  # CQG is only one column
    # Add more journals below. Can add more properties to each journal
}

width = jour_sizes["PRD"]["onecol"]

# Our figure's aspect ratio using the golden ratio
golden = (1 + 5 ** 0.5) / 2
my_height = my_width/golden

fig = plt.figure(figsize=(my_width,  my_height))