Figure Workflows¶

Single region plot¶

gf.plot("chr1:1,000,000-1,100,000")

Extend around region¶

gf.plot("chr1:1,000,000-1,050,000", extend=0.25)

Plot many regions¶

gf.plot_regions(["chr1:1,000,000-1,050,000", "chr1:1,060,000-1,110,000"], ncols=2)

plot_regions also accepts a BED path.

Plot by gene symbol¶

gf.plot_gene("GNAQ", extend=0.5)

Load from an IGV session¶

Convert a saved IGV .xml session directly into a GenomicFigure:

from plotnado import GenomicFigure

fig, locus = GenomicFigure.from_igv_session("session.xml")
fig.plot(locus)  # locus is the session's saved view region

Track colors, fixed scales (min/max), autoscale groups, and gene annotations are all preserved. The session locus is returned alongside the figure so you can use it directly or override it.

For lower-level access, parse_igv_session returns the intermediate IgvSession object (.template, .locus, .genome):

from plotnado import parse_igv_session, GenomicFigure

session = parse_igv_session("session.xml")
fig = GenomicFigure.from_template(session.template)
fig.plot(session.locus)

Edit tracks after building a figure¶

Access and mutate individual tracks by title (case-insensitive) or index:

fig["25_NK"].color = "steelblue"
fig[0].height = 2.0

Update a single track by key:

fig.update_track("CAT-MV411_H3K27ac", color="purple", max_value=500)

Update multiple tracks at once — omit key and optionally filter:

fig.update_track(height=0.2)                                    # all tracks
fig.update_track(track_type="bigwig", height=0.3)               # by type
fig.update_track(group="igv_group_3", max_value=1000.0)         # by autoscale group
fig.update_track(where=lambda t: t.title and "CD" in t.title, color="coral")

Remove a track:

fig.remove_track("25_NK")
fig.remove_track(0)

Add a track at the top or bottom (default):

fig.bigwig("new.bw", title="extra", position="top")
fig.genes("hg38", position="top")

All editing methods return self for chaining:

(fig
    .remove_track("01_HSC")
    .update_track(track_type="bigwig", height=0.25)
    .bigwig("new.bw", title="extra", position="top")
)

Save and load figure configs¶

gf.to_toml("figure.toml")
loaded = GenomicFigure.from_toml("figure.toml")
loaded.save("figure.png", "chr1:1,000,000-1,100,000")

See examples/recipes/02_theme_labels_toml.py for a full round-trip script.