CafePlotter

Table of contents

• Overview
• Installation
• Usage
• Output Contents

Overview

CAFE (Computational Analysis of gene Family Evolution) is a software to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences.

CAFE5 currently does not provide tools to visualize Expansion/Contraction of gene families on phylogenetic tree. To solve this issue, I developed CafePlotter, a tool for plotting CAFE5 gene family expansion/contraction result.

Installation

Python 3.8 or later is required for installation.

Install PyPI package:

pip install cafeplotter

Usage

Basic Command

cafeplotter -i [CAFE5 result directory] -o [Output directory]

Options

General Options:
  -i IN, --indir IN       CAFE5 result directory as input
  -o OUT, --outdir OUT    Output directory for plotting CAFE5 result
  --format                Output image format ('png'[default]|'jpg'|'svg'|'pdf')
  -v, --version           Print version information
  -h, --help              Show this help message and exit

Figure Appearence Options:
  --fig_height            Figure height per leaf node of tree (Default: 0.5)
  --fig_width             Figure width (Default: 8.0)
  --leaf_label_size       Leaf label size (Default: 12)
  --count_label_size      Gene count label size (Default: 8)
  --innode_label_size     Internal node label size (Default: 0)
  --p_label_size          Branch p-value label size (Default: 0)
  --ignore_branch_length  Ignore branch length for plotting tree (Default: OFF)
  --expansion_color       Plot color of gene family expansion (Default: 'red')
  --contraction_color     Plot color of gene family contraction (Default: 'blue')
  --dpi                   Figure DPI (Default: 300)

Example Command

User can download example dataset (singlelambda.zip):

cafeplotter -i ./examples/singlelambda -o ./singlelambda_plot --ignore_branch_length

Output Contents

• summary_all_gene_family.[png|jpg|svg|pdf]
  Summary of all expansion/contraction gene family result (from *_clade_result.txt)

  

• gene_family/{FamilyID}_gene_family.[png|jpg|svg|pdf]
  Significant expansion(red)/contraction(blue) gene family result

  

• result_summary.tsv (example)
  Significant expansion/contraction result summary for each family and taxon