openms-insight 0.1.0

Interactive visualization components for mass spectrometry data in Streamlit

OpenMS-Insight

Interactive visualization components for mass spectrometry data in Streamlit, backed by Vue.js.

Features

• Cross-component selection linking via shared identifiers
• Polars LazyFrame support for efficient data handling
• Automatic disk caching with config-based invalidation
• Table component (Tabulator.js) with filtering, sorting, go-to, pagination
• Line plot component (Plotly.js) with highlighting, annotations, zoom
• Heatmap component (Plotly scattergl) with multi-resolution downsampling
• Sequence view component for peptide/protein visualization

Installation

pip install openms-insight

Quick Start

import streamlit as st
import polars as pl
from openms_insight import Table, LinePlot, StateManager

# Create state manager for cross-component linking
state_manager = StateManager()

# Create a table - clicking a row sets the 'item' selection
table = Table(
    cache_id="items_table",
    data=pl.scan_parquet("items.parquet"),
    interactivity={'item': 'item_id'},
    column_definitions=[
        {'field': 'item_id', 'title': 'ID', 'sorter': 'number'},
        {'field': 'name', 'title': 'Name'},
    ],
)
table(state_manager=state_manager)

# Create a linked plot - filters by the selected 'item'
plot = LinePlot(
    cache_id="values_plot",
    data=pl.scan_parquet("values.parquet"),
    filters={'item': 'item_id'},
    x_column='x',
    y_column='y',
)
plot(state_manager=state_manager)

Cross-Component Linking

Components communicate through identifiers using two mechanisms:

• filters: INPUT - filter this component's data by the selection
• interactivity: OUTPUT - set a selection when user clicks

# Master table: no filters, sets 'spectrum' on click
master = Table(
    cache_id="spectra",
    data=spectra_data,
    interactivity={'spectrum': 'scan_id'},  # Click -> sets spectrum=scan_id
)

# Detail table: filters by 'spectrum', sets 'peak' on click
detail = Table(
    cache_id="peaks",
    data=peaks_data,
    filters={'spectrum': 'scan_id'},        # Filters where scan_id = selected spectrum
    interactivity={'peak': 'peak_id'},      # Click -> sets peak=peak_id
)

# Plot: filters by 'spectrum', highlights selected 'peak'
plot = LinePlot(
    cache_id="plot",
    data=peaks_data,
    filters={'spectrum': 'scan_id'},
    interactivity={'peak': 'peak_id'},
    x_column='mass',
    y_column='intensity',
)

---

Components

Table

Interactive table using Tabulator.js with filtering dialogs, sorting, pagination, and CSV export.

Table(
    cache_id="spectra_table",
    data=pl.scan_parquet("spectra.parquet"),
    interactivity={'spectrum': 'scan_id'},
    column_definitions=[
        {'field': 'scan_id', 'title': 'Scan', 'sorter': 'number'},
        {'field': 'rt', 'title': 'RT (min)', 'sorter': 'number', 'hozAlign': 'right'},
        {'field': 'precursor_mz', 'title': 'm/z', 'sorter': 'number'},
    ],
    index_field='scan_id',
    go_to_fields=['scan_id'],
    default_row=0,
    pagination=True,
    page_size=50,
)

LinePlot

Stick-style line plot using Plotly.js for mass spectra visualization.

LinePlot(
    cache_id="spectrum_plot",
    data=pl.scan_parquet("peaks.parquet"),
    filters={'spectrum': 'scan_id'},
    interactivity={'peak': 'peak_id'},
    x_column='mass',
    y_column='intensity',
    highlight_column='is_annotated',
    annotation_column='ion_label',
    title="MS/MS Spectrum",
    x_label="m/z",
    y_label="Intensity",
)

Heatmap

2D scatter heatmap using Plotly scattergl with multi-resolution downsampling for large datasets (millions of points).

Heatmap(
    cache_id="peaks_heatmap",
    data=pl.scan_parquet("all_peaks.parquet"),
    x_column='retention_time',
    y_column='mass',
    intensity_column='intensity',
    interactivity={'spectrum': 'scan_id', 'peak': 'peak_id'},
    min_points=30000,
    title="Peak Map",
    x_label="Retention Time (min)",
    y_label="m/z",
)

SequenceView

Peptide/protein sequence visualization with fragment ion matching.

SequenceView(
    cache_id="peptide_view",
    sequence="PEPTIDEK",
    observed_masses=[147.1, 244.2, 359.3, 456.4],
    peak_ids=[0, 1, 2, 3],
    precursor_mass=944.5,
    interactivity={'peak': 'peak_id'},
    title="Fragment Coverage",
)

---

Shared Component Arguments

All components accept these common arguments:

Argument	Type	Default	Description
cache_id	str	Required	Unique identifier for disk cache
data	pl.LazyFrame	None	Polars LazyFrame with source data
filters	Dict[str, str]	None	Map identifier -> column for filtering
interactivity	Dict[str, str]	None	Map identifier -> column for click actions
cache_path	str	"."	Base directory for cache storage

Rendering

All components are callable. Pass a StateManager to enable cross-component linking:

from openms_insight import StateManager

state_manager = StateManager()

table(state_manager=state_manager, height=300)
plot(state_manager=state_manager, height=400)

---

Development

Building the Vue Component

cd js-component
npm install
npm run build

Development Mode

cd js-component
npm run dev

# In another terminal:
export SVC_DEV_MODE=true
export SVC_DEV_URL=http://localhost:5173
streamlit run app.py