Skip to content

Phyllotaxis AnalysisLink

A Combinatorial Model of Phyllotaxis Perturbations in Arabidopsis thaliana.

DescriptionLink

This package provides tools for analyzing phyllotaxis patterns in plants, particularly focusing on perturbations in Arabidopsis thaliana. It implements algorithms for detecting and characterizing divergence angles and permutations in phyllotactic patterns.

InstallationLink

You can install the package using pip:

pip install phyllotaxis_analysis

Or directly from the source code:

git clone https://gitlab.inria.fr/mosaic/phyllotaxis_analysis.git
cd phyllotaxis_analysis
pip install .

DependenciesLink

To run the algorithms you will need:

  • Python >= 3.7
  • NumPy
  • SciPy

For the GUI:

  • PyQt5
  • Matplotlib

UsageLink

Basic usage example:

from phyllotaxis_analysis.analysis_functions import theoretical_divergence_angles, is_n_admissible

# Calculate theoretical divergence angles
permutationBlockMaxSize, canonicalAngle = 3, 137.5
angles, coefficients = theoretical_divergence_angles(permutationBlockMaxSize, canonicalAngle)

# Check if a sequence is n-admissible
seqTA = [137.5, 137.5, 275, 222.5, 275, 137.5]
result = is_n_admissible(seqTA, 137.5)

For more detailed examples, see the documentation.

LicenseLink

This project is licensed under the CeCILL-C License - see the LICENSE.txt file for details.

ReferencesLink

Refahi, Y., Farcot, E., Guédon, Y., Besnard, F., Vernoux, T., Godin, C. (2011). A Combinatorial Model of Phyllotaxis Perturbations in Arabidopsis thaliana. In: Giancarlo, R., Manzini, G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol. 6661. Springer, Berlin, Heidelberg. 10.1007/978-3-642-21458-5_28

Guédon, Y., Refahi, Y., Besnard, F., Farcot, E., Godin, C., Vernoux, T. (2013). Pattern identification and characterization reveal permutations of organs as a key genetically controlled property of post-meristematic phyllotaxis. Journal of Theoretical Biology, 338, 94-110. 10.1016/j.jtbi.2013.07.026