Bio components

Domain components for bioinformatics authors, wrapping 3Dmol.js/ProtVista/LocusZoom.js.

GWAS Association Plot (LocusZoom) ::locuszoom-assoc

Renders an interactive regional association plot for a genomic locus: GWAS -log10(p-value) points colored by linkage disequilibrium (LD), a recombination-rate overlay, and a gene track for the region. Use this when the author wants to show the association signal and gene context around a specific locus (e.g. a GWAS hit or a gene of interest), not for genome-wide/multi-locus comparisons (see locuszoom-gwas-catalog) or phenome-wide comparisons at a single variant (see locuszoom-phewas).

Prop Type Required Description
chrom string yes Chromosome name, without a "chr" prefix (e.g. "10").
start number yes Start position of the region to plot, in base pairs (GRCh37 coordinates).
end number yes End position of the region to plot, in base pairs (GRCh37 coordinates). Must be greater than start.

GWAS Association Plot with Catalog Annotations (LocusZoom) ::locuszoom-gwas-catalog

Same regional association plot as locuszoom-assoc (points colored by LD, recombination-rate overlay, gene track), plus known significant hits from the NHGRI-EBI GWAS Catalog labeled directly on the plot. Use this when the author wants to relate a signal to previously published GWAS hits in the same region — prefer locuszoom-assoc if that catalog context isn't needed, since this adds an extra data source and can be busier.

Prop Type Required Description
chrom string yes Chromosome name, without a "chr" prefix (e.g. "9").
start number yes Start position of the region to plot, in base pairs (GRCh37 coordinates).
end number yes End position of the region to plot, in base pairs (GRCh37 coordinates). Must be greater than start.

Phenome-Wide Association Plot (LocusZoom PheWAS) ::locuszoom-phewas

Renders a phenome-wide association scan (PheWAS) for a single variant: -log10(p-value) across many phenotypes/traits, colored by trait category, plus a gene track for context. Use this when the author wants to show how one specific variant associates across many phenotypes — this is the inverse of locuszoom-assoc/locuszoom-gwas-catalog, which show many variants across one region for a single phenotype.

Prop Type Required Description
variant string yes Variant identifier as "chrom:position_ref/alt" (e.g. "10:114758349_C/T"). The plot is centered on this variant with a fixed +/-250kb window.

GWAS Association Plot with Interval Annotations (LocusZoom) ::locuszoom-intervals

Same regional association plot as locuszoom-assoc (LD-colored points, recombination-rate overlay, gene track), plus an interval annotation track showing labeled genomic regions (e.g. chromatin states, regulatory elements) beneath the association points. Use this when the author wants to relate an association signal to annotated functional regions in the same locus — prefer locuszoom-assoc if that annotation track isn't needed.

Prop Type Required Description
chrom string yes Chromosome name, without a "chr" prefix (e.g. "10").
start number yes Start position of the region to plot, in base pairs (GRCh37 coordinates).
end number yes End position of the region to plot, in base pairs (GRCh37 coordinates). Must be greater than start.

95% Credible Set Association Plot (LocusZoom) ::locuszoom-credible-sets

Regional association plot that computes and highlights the 95% Bayesian credible set of likely-causal variants for the locus (derived from the association p-values themselves, using a fixed genome-wide significance threshold), alongside LD, recombination rate, and gene tracks. Use this when the author wants to narrow a signal down to its most probable causal variants, not just show the raw association — prefer locuszoom-assoc for a plain signal plot without that statistical layer.

Prop Type Required Description
chrom string yes Chromosome name, without a "chr" prefix (e.g. "16").
start number yes Start position of the region to plot, in base pairs (GRCh37 coordinates).
end number yes End position of the region to plot, in base pairs (GRCh37 coordinates). Must be greater than start.

Layered Multi-Phenotype Association Plot (LocusZoom) ::locuszoom-multi-pheno

Overlays association signals for four related metabolic-trait GWAS (fasting glucose, fasting insulin, triglycerides, total cholesterol — each a real published meta-analysis) as differently colored point layers on one association panel, with a shared gene track. Use this when the author wants to compare whether a locus affects several correlated metabolic phenotypes at once — for a single phenotype, use locuszoom-assoc instead. The phenotype set is fixed and cannot be changed via props.

Prop Type Required Description
chrom string yes Chromosome name, without a "chr" prefix (e.g. "10").
start number yes Start position of the region to plot, in base pairs (GRCh37 coordinates).
end number yes End position of the region to plot, in base pairs (GRCh37 coordinates). Must be greater than start.

Protein Sequence & Feature Viewer (ProtVista/UniProt) ::protvista

Renders UniProt sequence, domain, and feature tracks (variants, PTMs, structural coverage, etc.) for a protein. Use this when the author wants to show sequence-level annotation for a specific UniProt entry, not a 3D structure (see structure) or a single-variant/genomic-locus view (see the locuszoom-* components).

Prop Type Required Description
accession string yes A UniProt accession (e.g. "P05067").

3D Protein Structure Viewer (3Dmol.js) ::structure

Renders an interactive 3D viewer for a protein structure from the PDB, via 3Dmol.js. Use this when the author wants to show a specific solved/predicted 3D structure, not sequence-level annotation (see protvista) or a genomic-locus view (see the locuszoom-* components).

Prop Type Required Description
pdbid string yes A 4-character PDB entry ID (e.g. "1cbs").

Genome Browser (IGV.js) ::genome-browser

Renders a scrollable/zoomable genome-browser view of a locus — reference sequence plus the default gene annotation track, via IGV.js. Use this when the author wants to browse what is actually at a region, not a single plot type — for a GWAS association plot see the locuszoom-* components; for a 3D structure see structure. Only IGV.js's built-in reference genomes are supported (no custom track URLs) — see this package's README.

Prop Type Required Description
locus string yes Genomic region as "chrom:start-end", e.g. "chr7:140753336-140763336".
genome string no One of IGV.js's built-in genome IDs (e.g. "hg38", "hg19", "mm39"). Defaults to "hg38".

FASTA Sequence Viewer ::fasta

Renders a nucleotide/protein sequence with a position ruler, wrapped for readability, per-residue color coding (by base for nucleotide sequences, by side-chain property for protein), and optional residue-range highlighting. Use this for a short inline sequence the author is providing directly, not one fetched from an accession (see protvista for UniProt-backed sequence tracks).

Prop Type Required Description
sequence string yes The raw sequence (nucleotide or protein), whitespace is ignored.
id string no Optional sequence label, rendered as a ">id" header.
highlight string no Comma-separated 1-indexed residue ranges to highlight, e.g. "10-25,40-45".

Phylogenetic Tree Viewer (Newick) ::newick

Renders a small phylogenetic tree from Newick-format text as a rectangular cladogram. Use this for an author-provided tree topology, not a fetched one — there is no accession-based tree source yet.

Prop Type Required Description
tree string yes Newick-format tree string, e.g. "(A:0.1,(B:0.2,C:0.3):0.4);".
title string no Optional title rendered above the tree.

KEGG Pathway Diagram ::pathway

Renders a KEGG pathway diagram image for a given KEGG pathway ID. Use this when the author wants to show a biological pathway (metabolic, signaling, disease) as a whole map, not a single gene/protein/variant — see gene/protvista/structure/variant for those.

Prop Type Required Description
keggid string yes A KEGG pathway ID, e.g. "hsa04910" (human insulin signaling) or "map00010" (glycolysis, reference).
title string no Optional title rendered above the diagram.

Protein-Protein Interaction Network (STRING) ::interaction-network

Renders a protein-protein interaction network image for one or more genes/proteins, via the STRING database. Use this when the author wants to show what a gene/protein interacts with, not its own structure/sequence (see structure/protvista) or a pathway map (see pathway).

Prop Type Required Description
gene string yes One gene/protein identifier, or several comma-separated (e.g. "TP53" or "TP53,MDM2,BRCA1").
species number no NCBI taxonomy ID for the species (e.g. 9606 for human, 10090 for mouse). Defaults to 9606.
title string no Optional title rendered above the network.

Variant Card (ClinVar/dbSNP) ::variant

Renders a card of ClinVar/dbSNP annotation for a single variant, given its rsID — gene, hg38 position, allele, ClinVar clinical significance, associated conditions, and a CADD deleteriousness score where available. Use this for a single variant's own annotation, not a locus-wide association plot (see the locuszoom-* components) or a phenome-wide scan (see locuszoom-phewas).

Prop Type Required Description
rsid string yes A dbSNP rsID, e.g. "rs7903146".
title string no Optional title rendered above the card.