Metadata-Version: 2.1
Name: classconvergence
Version: 1.2
Summary: Plot the class distribution as a function of iteration from a Class2D or Class3D job from RELION
Home-page: https://github.com/Guillawme/classconvergence
Author: Guillaume Gaullier
Author-email: contact@gaullier.org
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/Guillawme/classconvergence/issues
Project-URL: Source, https://github.com/Guillawme/classconvergence
Keywords: cryo-EM class distribution plot visualization
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Environment :: Console
Classifier: Natural Language :: English
Requires-Python: >=3.9.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click (>=8.0.3)
Requires-Dist: matplotlib (>=3.4.3)
Requires-Dist: starfile (>=0.4.9)

# classconvergence

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4732050.svg)](https://doi.org/10.5281/zenodo.4732050)

Plot the class distribution as a function of iteration from a Class2D or Class3D
job from RELION.

This tool was tested with star files produced by RELION-3.1.0. Earlier versions
of RELION are not supported.

## Acknowledgments

I would not have been able to put this tool together without the
[`starfile`](https://github.com/alisterburt/starfile) library.

## Installation

I recommend to install this tool in a dedicated conda environment. You can
create one like so (replace `ENV_NAME` with the name you want to give to this
environment):

```
$ conda deactivate
$ conda create --name ENV_NAME python=3.9
$ conda activate ENV_NAME
```

Once the conda environment is active, you can install the tool with the
following command:

```
$ pip install classconvergence
```

## Usage

```
$ classconvergence --help
Usage: classconvergence [OPTIONS] <job_directory>

  Plot the class distribution as a function of iteration from a Class2D or
  Class3D job from RELION.

Options:
  -c, --count        Plot particle counts per class (default, same effect as
                     not passing any option).

  -p, --percent      Plot percentages of particles per class (default:
                     counts).

  -o, --output TEXT  File name to save the plot (optional: with no file name,
                     simply display the plot on screen without saving it;
                     recommended file formats: .png, .pdf, .svg or any format
                     supported by matplotlib).

  -h, --help         Show this message and exit.
```


