bio-data-visualization-genome-tracks

Version Compatibility

Reference examples tested with: GenomicRanges 1.54+, bedtools 2.31+, deepTools 3.5+

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 Track Visualization

"Plot genomic data tracks" → Create stacked track visualizations of coverage, peaks, annotations, and signals across a genomic region.

• Python: pyGenomeTracks, matplotlib with custom track panels
• R: Gviz::plotTracks() (Bioconductor)

pyGenomeTracks (Python/CLI)

# Create tracks configuration file
cat > tracks.ini << 'EOF'
[bigwig]
file = coverage.bw
title = Coverage
height = 4
color = #4DBBD5
min_value = 0

[spacer]
height = 0.5

[peaks]
file = peaks.bed
title = Peaks
color = #E64B35
height = 2
labels = false

[spacer]
height = 0.5

[genes]
file = genes.gtf
title = Genes
height = 5
fontsize = 10
style = flybase
color = #3C5488

[x-axis]
EOF

# Generate plot
pyGenomeTracks --tracks tracks.ini --region chr1:1000000-2000000 \
    --outFileName tracks.png --dpi 150

pyGenomeTracks with Multiple Samples

[sample1 coverage]
file = sample1.bw
title = Sample 1
height = 3
color = #4DBBD5
min_value = 0
max_value = auto

[sample2 coverage]
file = sample2.bw
title = Sample 2
height = 3
color = #E64B35
min_value = 0
max_value = auto

[sample1 peaks]
file = sample1_peaks.narrowPeak
title = Sample 1 Peaks
color = #4DBBD5
height = 1
file_type = narrowPeak

[sample2 peaks]
file = sample2_peaks.narrowPeak
title = Sample 2 Peaks
color = #E64B35
height = 1
file_type = narrowPeak

pyGenomeTracks Programmatic

import pygenometracks.tracks as pygtk

tracks = pygtk.PlotTracks('tracks.ini', fig_width=40, dpi=150)
tracks.plot('output.png', 'chr1', 1000000, 2000000)