Quickstart

This page builds a small oncoplot from an inline pandas DataFrame.

Input Data

Mutation input is one row per mutation event. At minimum, you need a sample column and a gene column. A mutation type column is strongly recommended.

import pandas as pd

mutations = pd.DataFrame(
    {
        "sample": ["S1", "S1", "S2", "S2", "S3", "S4"],
        "gene": ["TP53", "EGFR", "TP53", "PTEN", "PTEN", "EGFR"],
        "mutation_type": [
            "Missense_Mutation",
            "Frame_Shift_Del",
            "Nonsense_Mutation",
            "Splice_Site",
            "Missense_Mutation",
            "In_Frame_Del",
        ],
        "tooltip": [
            "S1 TP53 missense",
            "S1 EGFR frameshift deletion",
            "S2 TP53 nonsense",
            "S2 PTEN splice",
            "S3 PTEN missense",
            "S4 EGFR in-frame deletion",
        ],
    }
)

Interactive Plotly Plot

from pyoncoplot import oncoplot

result = oncoplot(
    mutations,
    gene_col="gene",
    sample_col="sample",
    mutation_type_col="mutation_type",
    tooltip_col="tooltip",
    top_n=10,
    draw_gene_bar=True,
    draw_tmb_bar=True,
    backend="plotly",
)

result.show()
result.save("quickstart.html")

Plotly output includes hover labels. Exported HTML also includes click-to-copy behavior unless copy_on_click="nothing" is used.

Static Matplotlib Plot

from pyoncoplot import OncoplotOptions, oncoplot

result = oncoplot(
    mutations,
    gene_col="gene",
    sample_col="sample",
    mutation_type_col="mutation_type",
    tooltip_col="tooltip",
    draw_gene_bar=True,
    draw_tmb_bar=True,
    backend="matplotlib",
    options=OncoplotOptions(width=900, height=520),
)

result.save("quickstart.png", dpi=120)

Result Object

oncoplot() returns an OncoplotResult with:

.figure: the backend figure object.
.prepared_data: the transformed data used by the renderer.
.show(): display interactive figures when the backend supports it.
.save(path, **kwargs): save HTML, PNG, SVG, PDF, or other backend-supported formats.
.to_html(...): Plotly-only HTML export.

Where To Go Next