scimorph 1.0.2

Scientific theme of Matplotlib for publication

scimorph: theme_publication

PyPI version
conda-forge version

Warning : The scimorph library requires LaTeX for math formatting. Install it using: sudo apt install texlive texlive-latex-extra texlive-fonts-recommended cm-super dvipng. : Starting with version 1.0.0, you must add import scimorph before setting the style with theme_publication('publication').

Matplotlib styles for scientific figures

This repo has Matplotlib styles to format your figures for scientific papers, presentations and theses.

You can find the full tutorials of scimorph here.

Getting Started

The easiest way to install scimorph is by using pip:

# to install the latest release (from PyPI)
pip install scimorph

# to install the latest commit (from GitHub)
pip install git+https://github.com/haihuilab/scimorph

# to clone and install from a local copy
git clone https://github.com/haihuilab/scimorph.git
cd scimorph
pip install -e .

From version v1.0.0 on, import scimorph is needed on top of your scripts so Matplotlib can make use of the styles.

Notes:

• scimorph-theme_publication requires matplotlib or seaborn

Using the Styles

"publication" is the primary style in this repo. Whenever you want to use it, simply add the following to the top of your python script:

import matplotlib.pyplot as plt
import scimorph

theme_publication('publication')

Examples

import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path
from scimorph.theme_publication import theme_publication
dir = Path.cwd()
print('parent dir: ',dir)

x = np.linspace(0, 2 * np.pi, 500)
y = np.sin(x)
# df = pd.DataFrame({'x': x, 'y': y})

theme_publication('publication', 
                    figsize='medium', 
                    fontsize=None, 
                    grid=True,
                    border=True)
plt.plot(x, y)
plt.xlabel('x')
plt.ylabel('y')
plt.savefig(f'{dir}/examples/plots/fig01a.jpg')
plt.show()

The basic publication style is shown below:

If you use scimorph in your paper/thesis, feel free to add it to the list!

Citing scimorph:

@article{scimorph,
  author       = {Haihui Zhang et al},
  title        = {haihuilab/scimorph},
  month        = Jan,
  year         = 2025,
  publisher    = {github},
  version      = {1.0.0},      
  url          = {https://github.com/haihuilab/scimorph}
}