bio-data-visualization-genome-browser-tracks

Version Compatibility

Reference examples tested with: GenomicRanges 1.54+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Genome Browser Tracks

"Create genome browser track visualizations" → Generate publication-quality track plots or automate IGV screenshots showing aligned reads, coverage, and annotations at specific loci.

• Python: pyGenomeTracks for static multi-track figures
• CLI: IGV batch scripting for screenshots

pyGenomeTracks INI Configuration

[x-axis]
where = top

[bigwig_coverage]
file = sample.bw
title = Coverage
height = 3
color = #4DBBD5
min_value = 0
max_value = auto

[spacer]
height = 0.5

[peaks]
file = peaks.bed
title = Peaks
color = #E64B35
height = 1
display = collapsed

[genes]
file = genes.gtf
title = Genes
height = 5
fontsize = 10
style = UCSC
color = navy

pyGenomeTracks Command

# Generate track plot
pyGenomeTracks --tracks tracks.ini --region chr1:1000000-2000000 \
    --outFileName region.png --dpi 300

# Multiple regions
for region in chr1:1000000-2000000 chr2:5000000-6000000; do
    pyGenomeTracks --tracks tracks.ini --region $region \
        --outFileName "${region//:/_}.png" --dpi 300
done

pyGenomeTracks Python API

import pygenometracks.tracks as pygtk
from pygenometracks import plotTracks

# Programmatic track configuration
tracks = '''
[x-axis]
where = top

[bigwig]
file = coverage.bw
title = ChIP-seq
height = 4
color = #4DBBD5

[bed]
file = peaks.narrowPeak
title = Peaks
height = 1
color = #E64B35
'''

# Write config and plot
with open('tracks.ini', 'w') as f:
    f.write(tracks)

# Using command line via subprocess
import subprocess
subprocess.run([
    'pyGenomeTracks',
    '--tracks', 'tracks.ini',
    '--region', 'chr1:1000000-2000000',
    '--outFileName', 'output.png',
    '--dpi', '300'
])