prs-ui 0.3.4

Reusable Reflex UI components for Polygenic Risk Score computation with PGS Catalog

prs-ui

Reusable Reflex UI components for Polygenic Risk Score (PRS) computation using the PGS Catalog.

Built on top of just-prs for the computation engine and reflex-mui-datagrid for data grid display.

Installation

pip install prs-ui

Running the Standalone App

uv run start

The launcher reads .env, resolves both the Reflex frontend port (PRS_UI_PORT, default 3000) and backend port (PRS_UI_BACKEND_PORT, default 8000), and passes the resolved pair explicitly to Reflex so another running Reflex app cannot shift only one side.

Quick Start

import polars as pl
import reflex as rx
from reflex_mui_datagrid import LazyFrameGridMixin
from prs_ui import PRSComputeStateMixin, prs_section


class MyAppState(rx.State):
    genome_build: str = "GRCh38"
    cache_dir: str = ""
    status_message: str = ""


class PRSState(PRSComputeStateMixin, LazyFrameGridMixin, MyAppState):
    def load_genotypes(self, parquet_path: str) -> None:
        lf = pl.scan_parquet(parquet_path)
        self.set_prs_genotypes_lf(lf)  # preferred: provide a LazyFrame
        self.prs_genotypes_path = parquet_path


def prs_page() -> rx.Component:
    return prs_section(PRSState)

Components

Component	Description
prs_workbench(source_section, prs_state, trait_state, mode_state, trait_selector, ...)	Unified single-tab layout: one shared genotype source + Select by PRS / Select by Trait sub-tabs, per-mode controls, compute button, and per-mode results
vcf_source_section(source_state)	Reference detachable genotype source: compact VCF upload + build detection + collapsed normalized preview. Swap it for your own source in a host app
prs_shared_build_bar(source_state)	Single genome-build selector that fans the build out to all consumer states
prs_section(state)	Older single-state section: build selector + score grid + compute button + progress + results
prs_build_selector(state)	Genome build dropdown (GRCh37/GRCh38)
prs_scores_selector(state)	MUI DataGrid for score selection. Selection (checkboxes + Select/Clear) is read-only and dimmed until genotypes are loaded, with an "upload a VCF" callout
prs_compute_button(state)	Compute button with disclaimer callout
prs_progress_section(state)	Progress bar and status text during computation
prs_results_table(state)	Results table with quality badges, interpretation cards, and CSV download

The genotype source is loosely coupled to the PRS logic: a source pushes a normalized genotypes parquet into each consumer via the additive load_genotypes(path) hook (and optionally set_genome_build(build)), so a host app can replace vcf_source_section / GenomicGridState with its own source (public genome, consumer-array file, pre-normalized parquet) without touching PRSComputeStateMixin. VCF normalization (not upload) is the slow step; it is content-aware cached (a fresh normalized parquet is reused) and shown via an indeterminate progress bar.

State Mixin

PRSComputeStateMixin provides all PRS computation logic as a Reflex state mixin. Mix it into your concrete state class alongside LazyFrameGridMixin to get the full PRS workflow.

The preferred input method is a polars LazyFrame via set_prs_genotypes_lf() -- memory-efficient and avoids re-reading VCF files on each computation. A parquet path (prs_genotypes_path) is supported as a fallback.

Documentation

See the just-prs documentation for the full Python API, CLI reference, and integration guide.