chromoplot 0.1.0

Flexible genome visualization toolkit for publication-ready figures

Chromoplot

Flexible genome visualization toolkit for publication-ready figures.

Features

• Track-based composition: Stack multiple data types vertically
• Format-agnostic: BED, GFF, PAF, BAM, VCF, bedGraph, bigWig
• Multiple layouts: Single region, whole genome, comparative synteny
• Publication-ready: Clean defaults optimized for print
• Fully customizable: Themes, colors, and per-track styling

Installation

pip install chromoplot

# With optional dependencies for BAM/bigWig support
pip install chromoplot[full]

Quick Start

Single Region

import chromoplot as cp

fig = cp.GenomeFigure("genome.fa.fai", region="chr1:1-10000000")
fig.add_track(cp.IdeogramTrack())
fig.add_track(cp.GeneTrack("genes.gff3", label="Genes"))
fig.add_track(cp.HaplotypeTrack("haplotypes.bed", label="Haplotypes"))
fig.add_track(cp.ScaleBarTrack())
fig.save("figure.pdf")

Whole Genome

import chromoplot as cp

coords = cp.GenomeCoordinates.from_fai("genome.fa.fai")
layout = cp.GenomeLayout(coords, arrangement='grid', n_cols=5)
layout.add_track(cp.IdeogramTrack())
layout.add_track(cp.HaplotypeTrack("haplotypes.bed"))
layout.save("genome_wide.pdf")

Comparative Synteny

import chromoplot as cp

ref_coords = cp.GenomeCoordinates.from_fai("ref.fa.fai")
query_coords = cp.GenomeCoordinates.from_fai("query.fa.fai")

layout = cp.ComparativeLayout(
    ref_coords, query_coords,
    ref_region="chr1", query_region="chr1"
)
layout.add_ref_track(cp.IdeogramTrack())
layout.add_ref_track(cp.GeneTrack("ref_genes.gff3"))
layout.add_synteny_track(cp.SyntenyTrack("alignment.paf"))
layout.add_query_track(cp.GeneTrack("query_genes.gff3"))
layout.add_query_track(cp.IdeogramTrack())
layout.save("synteny.pdf")

Command Line

# Single region plot
chromoplot plot -r genome.fa.fai --region chr1:1-10000000 \
    --gff genes.gff3 --haplotypes haplotypes.bed -o figure.pdf

# Whole genome plot
chromoplot genome -r genome.fa.fai --haplotypes haplotypes.bed -o genome.pdf

# Comparative synteny plot
chromoplot comparative --ref-fai ref.fa.fai --query-fai query.fa.fai \
    --synteny alignment.paf --ref-region chr1 --query-region chr1 -o synteny.pdf

# From YAML config
chromoplot from-config config.yaml -o figure.pdf

Available Tracks

Track	Description	Input Formats
IdeogramTrack	Chromosome backbone	(none)
GeneTrack	Gene models with exons	GFF3, GTF
FeatureTrack	Generic features	BED
HaplotypeTrack	Haplotype blocks	BED (phaser output)
AlignmentTrack	Sequence alignments	PAF
DepthTrack	Read coverage	BAM, bedGraph, bigWig
SignalTrack	Continuous signal	bedGraph, bigWig
VariantTrack	Variant positions	VCF
SyntenyTrack	Synteny ribbons	PAF, SyRI, MCScanX
ScaleBarTrack	Scale reference	(none)
AnnotationTrack	Text labels	TSV

Themes

# Built-in themes
fig = cp.GenomeFigure(..., theme='publication')  # Default
fig = cp.GenomeFigure(..., theme='presentation')
fig = cp.GenomeFigure(..., theme='minimal')
fig = cp.GenomeFigure(..., theme='dark')

# Custom theme
my_theme = cp.Theme(
    figure_facecolor='white',
    title_fontsize=14,
    label_fontsize=10,
)
cp.register_theme('my_theme', my_theme)

Color Palettes

# Get palette
colors = cp.get_palette('categorical', n=5)
colors = cp.get_palette('founder_default')
colors = cp.get_palette('maize_heterotic')

# Founder colors for haplotype tracks
color_map = cp.founder_colors(['B73', 'Mo17', 'W22'])

# Maize NAM colors (by heterotic group)
color_map = cp.maize_nam_colors(['B73', 'Mo17', 'CML247'])

License

MIT License