hoodini-viz API Reference

Auto-generated API documentation.

React Components

Main components exported by hoodini-viz for building genomic neighborhood visualizations.

<HoodiniDashboard />

HoodiniDashboard - Complete genomic neighborhood visualization dashboard.

Provides:

• Automatic data loading (Parquet/TSV)
• Sidebar with all controls
• HoodiniViz visualization
• DataGrid for tabular views
• Full theme support
• Imperative API via ref

Import:

import { HoodiniDashboard } from 'hoodini-viz';

Optional Props:

<HoodiniViz />

Import:

import { HoodiniViz } from 'hoodini-viz';

Optional Props:

Component Props

Prop interfaces for the React components.

HoodiniDashboardProps

Props for HoodiniDashboard component

HoodiniVizProps

Props for the HoodiniViz component.

HoodiniViz is the core visualization component that renders phylogenetic trees, genomic neighborhoods, protein domains, and homology links using deck.gl.

Configuration

Configuration interfaces for customizing visualization behavior.

DashboardPaletteConfig

Palette configuration

NucleotideLinkConfig

Nucleotide link visualization config

ProteinLinkConfig

Protein link visualization config

StyleConfig

Style configuration for visual layers

VizNucleotideLinkConfig

Configuration for nucleotide link visualization

VizPaletteConfig

Palette configuration for coloring

VizProteinLinkConfig

Configuration for protein link visualization

Data Types

Data structures for passing genomic data to components.

DataPaths

Data paths for loading genomic data. Supports both Parquet and TSV/text formats. If a parquet path fails, will try the corresponding text path.

GFFFeatureData

GFF Feature representing a gene or genomic feature

HoodData

Hood (genomic neighborhood) definition

NucleotideLinkData

Nucleotide-level synteny link

ParsedData

Parsed data available after loading

ProteinLinkData

Protein-protein homology link

Other Interfaces

FormatPreset

HoodiniDashboardRef

Methods exposed via ref

InitialState

Initial state configuration

Type Aliases

ColorMap

Color map for entities - maps entity ID to RGBA color

type ColorMap = Record<string, RGBAColor> | Map<string, RGBAColor> | None

RGBAColor

RGBA color as [r, g, b, a] where each value is 0-255

type RGBAColor = [number, number, number, number]

VisualizationConfig

Type for the complete visualization configuration

type VisualizationConfig = any

VizRGBAColor

RGBA color as [r, g, b, a] where each value is 0-255

type VizRGBAColor = [number, number, number, number]

Model Classes

Internal model classes for representing genomic data structures.

Domain

Methods:

• createDomainPolygon()

  function createDomainPolygon(g: any, domainStart: any, domainEnd: any): any[][]

• getConvexGenePolygon()

  function getConvexGenePolygon(g: any): any[][]

• interpolateOnLine()

  function interpolateOnLine(line: any, t: any): any[]

• normalize()

  function normalize(v: any): number[]

• perpVector()

  function perpVector(p0: any, p1: any): number[]

• setParentGene()

  function setParentGene(gene: any): void

• updatePolygon()

  function updatePolygon(): void

Gene

Methods:

• addDomain()

  function addDomain(domain: any): void

• computeCenterLine()

  function computeCenterLine(): any[]

• setTrackY()

  function setTrackY(y: any): void

• updatePolygon()

  function updatePolygon(): void

GenomeView

Methods:

• addDomainMetadata()

  function addDomainMetadata(domainMetadata: any): void

• addDomains()

  function addDomains(domainsByGene: any): void

• addFeatures()

  function addFeatures(gffFeatures: any): void

• addNucleotideLinks()

  function addNucleotideLinks(links: any, color: number[], adjacencyN: number): void

• addProteinLinks()

  function addProteinLinks(links: any, color: number[], adjacencyN: number): void

• alignAllToCenter()

  function alignAllToCenter(): void

• alignAllToEnd()

  function alignAllToEnd(): void

• alignAllToStart()

  function alignAllToStart(): void

• alignByDefaultGenes()

  function alignByDefaultGenes(): void

• alignCluster()

  function alignCluster(clusterId: any): void

• applyDomainPalette()

  function applyDomainPalette(paletteConfig: any): void

• applyHoods()

  function applyHoods(hoods: any): void

• applyNucleotideLinkColors()

  function applyNucleotideLinkColors(colorConfig: any): void

• applyProteinLinkColors()

  function applyProteinLinkColors(colorConfig: any): void

• buildEdgesWithMetadata()

  function buildEdgesWithMetadata(): any

• buildNodePoints()

  function buildNodePoints(selectedNode: any, colorLeavesBy: any): any

• buildPhyloLabels()

  function buildPhyloLabels(phyloLabelPosition: string): any

• buildScaleBar()

  function buildScaleBar(): any[]

• computeGenePrevalence()

  function computeGenePrevalence(categoryField: string): Map<any, any>

• computeTrackPositions()

  function computeTrackPositions(): void

• fadeColor()

  function fadeColor(color: any, factor: any): any[]

• filterBySelectedNode()

  function filterBySelectedNode(selectedNode: any): object

• flipTrack()

  function flipTrack(hood_id: any): void

• flipTrackState()

  function flipTrackState(hood_id: any): void

• flipTrackStateWithCentering()

  function flipTrackStateWithCentering(hood_id: any): void

• flipTrackToggle()

  function flipTrackToggle(hood_id: any): void

• getAllDomains()

  function getAllDomains(): any

• getAllNcRNAs()

  function getAllNcRNAs(): unknown[]

• getAllNonCodingFeatures()

  function getAllNonCodingFeatures(): unknown[]

• getAllRegions()

  function getAllRegions(): unknown[]

• getClusterSummary()

  function getClusterSummary(): any

• getGeneIdFromAttributes()

  function getGeneIdFromAttributes(attrs: any): any

• getHoodIdFromSeqid()

  function getHoodIdFromSeqid(seqid: any): any

• getHoodIdsFromSeqid()

  function getHoodIdsFromSeqid(seqid: any): any

• getNodeDescendantLeaves()

  function getNodeDescendantLeaves(node: any): any

• getNucleotidePolygons()

  function getNucleotidePolygons(): any[]

• getProteinPolygons()

  function getProteinPolygons(): any[]

• getRegionPolygons()

  function getRegionPolygons(): any[]

• getSeqidFromHoodId()

  function getSeqidFromHoodId(hood_id: any): any

• getTrackAnchor()

  function getTrackAnchor(hood_id: any): number

• getTrackY()

  function getTrackY(seqid: any): any

• getTrackYByHoodId()

  function getTrackYByHoodId(hood_id: any): any

• initGenes()

  function initGenes(): void

• setNcRNAColorsWithPalette()

  function setNcRNAColorsWithPalette(paletteConfig: any): void

• setProteinClusters()

  function setProteinClusters(clusterMap: any): void

• setProteinClustersWithPalette()

  function setProteinClustersWithPalette(clusterMap: any, paletteConfig: any): void

• setRegionColorsWithPalette()

  function setRegionColorsWithPalette(paletteConfig: any): void

• shiftTrack()

  function shiftTrack(hood_id: any, delta: any): void

• shiftTrackMinus1kb()

  function shiftTrackMinus1kb(hood_id: any): void

• shiftTrackPlus1kb()

  function shiftTrackPlus1kb(hood_id: any): void

• toggleTrackFlip()

  function toggleTrackFlip(hood_id: any): void

• updateGlobalBounds()

  function updateGlobalBounds(): void

• updateLinkPositions()

  function updateLinkPositions(): void

• flipCoordinate()

  function flipCoordinate(x: any, anchor: any): number

• getGeneVisualX()

  function getGeneVisualX(gene: any, genomeView: any): number

• getTransformedXUnified()

  function getTransformedXUnified(x: any, anchor: any, offset: any, flipped: any): any

PhyloNode

Methods:

• getLeaves()

  function getLeaves(): any

PhyloTree

Methods:

• assignInternalX()

  function assignInternalX(node: any): any

• assignX()

  function assignX(leaves: any): void

• buildEdges()

  function buildEdges(): any[]

• collectAll()

  function collectAll(): void

• computeDistances()

  function computeDistances(): void

• getLeafNodes()

  function getLeafNodes(): any

• ladderize()

  function ladderize(ascending: boolean): void

  Ladderize the tree by sorting branches at each node by the number of descendant leaves. This produces a cleaner visual representation matching Taxonium’s algorithm exactly. Uses iterative traversal to avoid stack overflow on large trees.

• layout()

  function layout(leavesOrder: any): void

• makeUltrametric()

  function makeUltrametric(): void

  Convert tree to ultrametric format where all leaves are equidistant from the root This adjusts branch lengths to make the tree ultrametric while preserving topology

• parseNewick()

  function parseNewick(s: any): PhyloNode

• scaleY()

  function scaleY(): void

• setParents()

  function setParents(): void

Utility Functions

getPaletteColors

function getPaletteColors(paletteName: any, numColors: any, reverse: boolean): any

getQualitativePalettes

function getQualitativePalettes(minColors: number, maxColors: number): any

getSequentialPalettes

function getSequentialPalettes(minColors: number, maxColors: number): any

Constants

DEFAULT_CONFIG

const DEFAULT_CONFIG: object

FORMAT_PRESETS

const FORMAT_PRESETS: FormatPreset[]