gwplot

gwplot is a plotting library for genomics data and a Python interface to GW, a high-performance interactive genome browser.

Features of gwplot:

  • Very fast visualisation of genomics data (BAM/CRAM, VCF, BED, and other formats)
  • Customisable themes and colors for creating high-quality visualisations
  • Multi-regions and data tracks for comparative genomics
  • Flexible output formats including PNG, PDF, SVG, JPEG, and NumPy arrays for further processing
  • Built-in access to common reference genomes
  • Integration with pysam, matplotlib, jupyter and pillow
  • Interactive mode for creating dynamic apps

Install from PyPI:

pip install gwplot

A quick example:

from gwplot import Gw

# Initialise with a reference genome
gw = Gw("hg38")

# Add a BAM file and a region to visualise
gw.add_bam("a.bam")
gw.add_region("chr1", 1000000, 1100000)

# Draw and save an image
gw.save_pdf("region.pdf")

# Display the image to your screen
gw.show()

gwplot also integrates with other Python libraries such as pysam:

from gwplot import Gw
import pysam

# Define a region of interest
roi = ("chr1", 1, 20000)

# Fetch some reads using pysam
a = list(pysam.AlignmentFile("a.bam").fetch(*roi))

with Gw("hg38") as gw:
    
    # Let Gw know which bam file and region to display
    gw.add_bam("a.bam")
    gw.add_region(*roi)
    
    # Gw uses the bam1_t* pointer straight from pysam
    gw.add_pysam_alignments(a)
    gw.show()

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