Track Catalog

Choose a track by the visual question you need to answer. The tables are compact; the examples show the actual rendered behavior.

Signal tracks

from plotnado import GenomicFigure
from plotnado.examples import REGION, signal
# signal() → DataFrame(chrom, start, end, value) — replace with a BigWig path/URL or DataFrame

fig = GenomicFigure(track_height=1.15)
fig.scalebar()
fig.bigwig(signal(phase=0.0), title="fill", style="fill", color="#1f77b4")
fig.bigwig(signal(phase=0.8), title="fragment", style="fragment", color="#d62728")
fig.bigwig(signal(phase=1.6), title="scatter", style="scatter", color="#2ca02c", scatter_point_size=10)
fig.bigwig(signal(phase=2.4), title="std", style="std", color="#9467bd")
fig.plot(REGION)

Track / aliases	Use when	Input
bigwig, bw, signal, bedgraph	You have one continuous signal.	BigWig path/URL or table with chrom, start, end, value.
overlay, bigwig_overlay	Several signals share one y-axis.	List of signal tables, paths, or compatible tracks.
bigwig_collection	You need compact multi-sample signal display.	BigWig file list.
bigwig_diff	You need a difference panel between two files.	Two BigWig sources.

There is no separate GenomicFigure.bedgraph() method; bedGraph-like inputs use bigwig.

Pass n_bins=N or bin_size=B to any bigwig-family track to rebin to a fixed resolution. Bins are computed as weighted averages of overlapping source intervals and work for both BigWig files and DataFrames.

Interval, peak, and link tracks

from plotnado import GenomicFigure
from plotnado.examples import REGION, intervals, links, narrowpeaks
# intervals() → DataFrame(chrom, start, end, name) — replace with a BED/BigBed path, URL, or DataFrame
# narrowpeaks() → DataFrame(chrom, start, end, name, score, strand, signalValue, pValue, qValue, peak) — replace with a .narrowPeak path or DataFrame
# links() → DataFrame(chrom1, start1, end1, chrom2, start2, end2, score) — replace with a BEDPE path or DataFrame

fig = GenomicFigure(track_height=1.1)
fig.bed(intervals(), title="BED", display="expanded", show_labels=True)
fig.narrowpeak(narrowpeaks(), title="narrowPeak", color_by="signalValue", cmap="Oranges", show_summit=True)
fig.links(links(), title="Links", color_by_score=True, cmap="viridis")
fig.axis()
fig.plot(REGION)

Track / aliases	Use when	Input
bed, annotation, unknown	You need intervals such as peaks, enhancers, regions, or labels.	BED/BigBed path or table with chrom, start, end.
narrowpeak	You have ENCODE narrowPeak data and want score/summit display.	narrowPeak path or table.
genes, gene	You need gene models for context.	Built-in genome name or compatible annotation data.
links	You need loops or paired anchors.	BEDPE-like table with chrom1, start1, end1, chrom2, start2, end2.
highlight	You want a shaded region behind tracks.	Region string or BED-like intervals.
hline, vline	You need threshold or coordinate markers.	Numeric y-value or genomic coordinate.

Structural tracks

Track / aliases	Use when
scalebar, scale	You want a visual distance cue.
axis	You want exact coordinate ticks.
spacer	You need blank vertical separation.

Optional tracks

These track families are available only when their optional dependencies and data formats are installed.

Track / aliases	Dependency/data gate	Use when
cooler, cooler_average	cooler-compatible files and optional matrix dependencies.	Hi-C/contact matrix panels.
capcruncher	CapCruncher output and optional dependencies.	Viewpoint-style capture contact summaries.
quantnado_coverage, quantnado_stranded_coverage, quantnado_methylation, quantnado_variant	QuantNado datasets and optional dependencies.	Coverage, methylation, and variant tracks from QuantNado stores.

Runtime lookup

from plotnado import GenomicFigure

GenomicFigure.available_track_aliases()
GenomicFigure.track_options("bigwig")
GenomicFigure.track_options_markdown("genes")

See Compact Options for a small rendered lookup page.