Example Coverage¶
This page maps track types to runnable examples and rendered outputs.
The default run of examples/run_examples.py replays the local example set. Remote Blueprint bigwig_collection / bigwig_diff coverage is opt-in with python examples/run_examples.py --include-remote because those scripts stream public BigWig files instead of checking large fixtures into the repo.
Rendered PNG outputs are written into examples/output/ and synced into docs/images/examples/, so the gallery below shows the same results produced by the current code.
Runnable script coverage¶
Runnable Example Gallery¶
Basic figure¶
Minimal scale bar, axis, genes, and one in-memory signal track.
Source: examples/basic_figure.py
Advanced features¶
Autocolor, highlight overlays, interval tracks, grouped autoscaling, and reference lines in one figure.
Source: examples/advanced_features.py
Quickstart first plot¶
The minimal quickstart script used from the installation guide.
Source: examples/quickstart/01_first_plot.py
Alias and options discovery¶
Demonstrates available_track_aliases() and track_options(...) and saves a small multi-track plot.
Source: examples/quickstart/02_aliases_and_options.py
BigWig styles¶
Compares fill, fragment, scatter, and std BigWig render modes.
Source: examples/tracks/01_bigwig_styles.py
BED and narrowPeak¶
Compares stacked BED intervals with score-colored narrowPeak rendering.
Source: examples/tracks/02_bed_and_narrowpeak.py
Links, hline, and vline¶
Shows BEDPE-style links together with horizontal and vertical annotation lines.
Source: examples/tracks/03_links_annotations.py
BigWig collection and diff¶
Fetches two public Blueprint plasma-cell RNA BigWigs once, stages tiny local crops for the target window in a temporary directory, then renders a bigwig_collection panel and a matching bigwig_diff panel from those local files.
Source: examples/tracks/04_bigwig_collection_and_diff.py
Cooler and cooler_average¶
Uses the checked-in GM12878 cooler fixture for a direct matrix view plus a simple averaged view built from the same file twice.
Source: examples/tracks/05_matrix_tracks.py
CapCruncher viewpoint matrix¶
Uses the checked-in reporters-store fixture and resolves the Slc25A37 viewpoint to the cooler group inside the HDF5 container.
Source: examples/tracks/05_matrix_tracks.py
QuantNado coverage and stranded coverage¶
Uses local on-disk QuantNado fixtures to render real ATAC coverage and stranded RNA signal.
Source: examples/tracks/06_quantnado_tracks.py
QuantNado methylation and variant tracks¶
The same script also renders file-backed methylation and variant panels from the compact test fixtures.
Source: examples/tracks/06_quantnado_tracks.py
Overlay, autoscale, and highlight¶
Demonstrates a shared overlay panel, grouped autoscaling, and region highlighting.
Source: examples/recipes/01_autoscale_overlay_highlight.py
Theme, labels, and TOML round-trip¶
Applies the publication theme, saves a TOML figure definition, and reloads it to render again.
Source: examples/recipes/02_theme_labels_toml.py
Reloaded from TOML:
Gene label strategies¶
Compares staggered, suppressed, and auto-expanded gene label placement strategies.
Source: examples/recipes/03_gene_label_strategies.py
Validate option coverage quickly¶
Use runtime metadata to inspect every field (track, aesthetics, label):
from plotnado import GenomicFigure
for alias in sorted(GenomicFigure.available_track_aliases()):
print(alias)
GenomicFigure.track_options(alias)
For full generated tables, see Aesthetics Reference.