{"id":19234310,"url":"https://github.com/moshi4/cafeplotter","last_synced_at":"2025-04-21T05:30:43.010Z","repository":{"id":101661928,"uuid":"609094225","full_name":"moshi4/CafePlotter","owner":"moshi4","description":"A tool for plotting CAFE5 gene family expansion/contraction 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CafePlotter\n\n![Python3](https://img.shields.io/badge/Language-Python3-steelblue)\n![OS](https://img.shields.io/badge/OS-_Windows_|_Mac_|_Linux-steelblue)\n![License](https://img.shields.io/badge/License-MIT-steelblue)\n[![Latest PyPI version](https://img.shields.io/pypi/v/cafeplotter.svg)](https://pypi.python.org/pypi/cafeplotter)\n[![CI](https://github.com/moshi4/CafePlotter/actions/workflows/ci.yml/badge.svg)](https://github.com/moshi4/CafePlotter/actions/workflows/ci.yml)\n\n## Table of contents\n\n- [Overview](#overview)\n- [Installation](#installation)\n- [Usage](#usage)\n- [Output Contents](#output-contents)\n\n## Overview\n\nCAFE (Computational Analysis of gene Family Evolution) is a software to analyze changes in gene family size in a way\nthat accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences.\n\n[CAFE5](https://github.com/hahnlab/CAFE5) currently does not provide tools to visualize Expansion/Contraction of gene families on phylogenetic tree.\nTo solve this issue, I developed CafePlotter, a tool for plotting CAFE5 gene family expansion/contraction result.\n\n## Installation\n\n`Python 3.8 or later` is required for installation.\n\n**Install PyPI package:**\n\n    pip install cafeplotter\n\n## Usage\n\n### Basic Command\n\n    cafeplotter -i [CAFE5 result directory] -o [Output directory]\n\n### Options\n\n    General Options:\n      -i IN, --indir IN       CAFE5 result directory as input\n      -o OUT, --outdir OUT    Output directory for plotting CAFE5 result\n      --format                Output image format ('png'[default]|'jpg'|'svg'|'pdf')\n      -v, --version           Print version information\n      -h, --help              Show this help message and exit\n\n    Figure Appearence Options:\n      --fig_height            Figure height per leaf node of tree (Default: 0.5)\n      --fig_width             Figure width (Default: 8.0)\n      --leaf_label_size       Leaf label size (Default: 12)\n      --count_label_size      Gene count label size (Default: 8)\n      --innode_label_size     Internal node label size (Default: 0)\n      --p_label_size          Branch p-value label size (Default: 0)\n      --ignore_branch_length  Ignore branch length for plotting tree (Default: OFF)\n      --expansion_color       Plot color of gene family expansion (Default: 'red')\n      --contraction_color     Plot color of gene family contraction (Default: 'blue')\n      --dpi                   Figure DPI (Default: 300)\n\n### Example Command\n\nUser can download example dataset ([singlelambda.zip](https://github.com/moshi4/CafePlotter/raw/main/examples/singlelambda.zip)):\n\n    cafeplotter -i ./examples/singlelambda -o ./singlelambda_plot --ignore_branch_length\n\n## Output Contents\n\n- **summary_all_gene_family.[png|jpg|svg|pdf]**  \n  Summary of all expansion/contraction gene family result (from `*_clade_result.txt`)\n\n  ![summary_all_gene_family.png](https://raw.githubusercontent.com/moshi4/CafePlotter/main/examples/images/summary_all_gene_family.png)\n\n- **gene_family/{FamilyID}_gene_family.[png|jpg|svg|pdf]**  \n  Significant expansion(*red*)/contraction(*blue*) gene family result  \n\n  ![gene_family.png](https://raw.githubusercontent.com/moshi4/CafePlotter/main/examples/images/gene_family/2_gene_family.png)\n\n- **result_summary.tsv** ([example](https://raw.githubusercontent.com/moshi4/CafePlotter/main/examples/result_summary.tsv))  \n  Significant expansion/contraction result summary for each family and taxon\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoshi4%2Fcafeplotter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoshi4%2Fcafeplotter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoshi4%2Fcafeplotter/lists"}