Plotting

Plotting (prot2exon plot)

Once you have an isoform_structure.tsv from Mapping, prot2exon plot renders it as a static figure (matplotlib) or as an interactive viewer (plotly or a self-contained vanilla-JS viewer). The plotter reads the TSV directly and never re-derives coordinates from the genome, so anything you can express by editing the table is plottable.

Static figures

CLI

Render a single query to a vector PDF:

prot2exon plot \
    --isoform results/isoform_structure.tsv \
    --input-id TP53_DBD \
    --out tp53.pdf

The output format follows the file extension (.pdf, .png, or .svg). To render every input_id in the TSV at once, use --all; with a .pdf target this becomes a single multipage PDF (one query per page), while a .png/.svg target writes one file per query named base.<input_id>.ext:

prot2exon plot --isoform results/isoform_structure.tsv --all --out queries.pdf   # multipage PDF
prot2exon plot --isoform results/isoform_structure.tsv --all --out queries.png   # queries.TP53_DBD.png, ...

Python

From a MappingResult (or an isoform DataFrame, or a path to the TSV):

import prot2exon as p2e

result = p2e.map_query("ENSP00000269305", 10, 50, "TP53_DBD", index="human.idx")
p2e.plot(result, input_id="TP53_DBD", out="tp53.pdf")

p2e.plot() returns the matplotlib Figure (useful when you pass neither out nor an HTML target). For batches, p2e.plot_all(source, out="queries.pdf") mirrors --all. See Python API for the full client.

Arguments

Flag / kwarg	Default	Effect
--isoform FILE	required	Path to the isoform_structure.tsv to plot.
--input-id ID	—	Render a single query (mutually exclusive with --all).
--all	—	Render every input_id; multipage PDF if --out ends in .pdf, else one file per query.
--out FILE	—	Static matplotlib output; format from the .pdf/.png/.svg extension.
--title STR	derived	Override the auto-generated title.
--width, --height	12, 2.6	Figure size in inches.
--no-highlight	off	Don't color CDS-in-domain segments red.
--no-introns	off	Hide intron lines.
--no-utr	off	Hide UTR boxes.
--spliced	off	Concatenate non-intron features in translation order (no introns).
--compact-genomic	off	Genomic order, but clamp each intron to a fixed display width (best for long-intron genes); CDS/UTR stay at true bp scale with a // compression mark. Mutually exclusive with --spliced.

The Python plot() / plot_all() functions accept the same toggles as keyword arguments (input_id, out, title, width, height, show_introns, show_utr, highlight_domain, spliced, compact_genomic).

Interactive viewers

CLI

Two interactive paths share the same command; the renderer is chosen by the output flag:

# plotly HTML (CDN-backed; hover tooltips and a bottom rangeslider)
prot2exon plot --isoform results/isoform_structure.tsv --input-id TP53_DBD \
    --html tp53.html

# self-contained vanilla-JS viewer (no CDN, single offline file)
prot2exon plot --isoform results/isoform_structure.tsv --input-id TP53_DBD \
    --html-interactive tp53.html \
    --link-template 'https://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?p={protein_id}'

--html needs plotly installed (pip install "prot2exon[html]"); --html-interactive has no JS dependencies. You can pass both alongside --out in one run. The standalone viewer supports box-zoom (drag to zoom into a genomic range), shift-drag to pan, mouse-wheel zoom, double-click to reset, a draggable minimap, UTR rendering with strand arrows, and a Compact / True-genomic layout toggle. --link-template adds a clickable linkout next to the title using the placeholders {protein_id}, {gene_name}, {transcript_id}, {chrom}, {start}, {end}.

With --all, each interactive flag writes one file per query (base.<input_id>.ext).

Python

For a single isoform, obtain the segments from a result and embed the viewer inline in a notebook:

import prot2exon as p2e
from prot2exon.plot import _segments_from_dataframe

result = p2e.map_query("ENSP00000269305", 10, 50, "TP53_DBD", index="human.idx")
segments = _segments_from_dataframe(result.isoform)["TP53_DBD"]

p2e.render_interactive_jupyter(segments, plot_height=160)

For several isoforms stacked in one viewer, pass the whole dict[input_id -> segments] to the stack variant:

segs_by_id = _segments_from_dataframe(result.isoform)
p2e.render_interactive_jupyter_stack(segs_by_id, plot_height=40)

To write standalone HTML files instead of embedding inline, use the file builders p2e.render_interactive_html(segments, "tp53.html") and p2e.render_interactive_html_stack(segs_by_id, "stack.html"). See Tutorials and Notebooks for end-to-end notebook examples.

Arguments

Flag / kwarg	Default	Effect
--html FILE	—	plotly interactive HTML (CDN-backed); requires plotly.
--html-interactive FILE	—	Self-contained vanilla-JS viewer (no CDN, offline-capable).
--link-template URL / link_template=	—	External linkout next to the title (HTML viewers only); placeholders {protein_id}, {gene_name}, {transcript_id}, {chrom}, {start}, {end}.
--height N (CLI)	2.6	matplotlib figure height in inches (static path).
plot_height= (Python)	140 single / 40 stack	Main-track height in pixels for the Jupyter / standalone viewers.
height= (Python)	auto	Pin the Jupyter iframe height in px (for static exports where the auto-resize handshake can't fire).

The hidden --html-tfregdb2 CLI flag and the render_tfregdb2_* Python functions are deprecated aliases for the --html-interactive / render_interactive_* names, kept only for backwards compatibility and slated for removal.