ProjectionReader

Class for reading UMAP, t-SNE, PCA and other dimensionality reduction coordinates.

Access

const reader = await CloupeReader.open(file);
const projectionReader = reader.projections;

Properties

availableProjections

get availableProjections(): string[]

Returns available projection names.

Methods

read()

async read(name: string): Promise<Projection>

Reads projection by name.

Parameters

Name	Type	Description
name	string	Projection name (e.g., 'UMAP', 't-SNE')

Examples

const umap = await reader.projections.read("UMAP");

console.log(`Dimensions: ${umap.dimensions}`);
console.log(`Points: ${umap.numPoints}`);

// X, Y coordinate arrays
const x = umap.coordinates[0]; // Float64Array
const y = umap.coordinates[1]; // Float64Array

readDefault()

async readDefault(): Promise<Projection | null>

Returns the default projection. Returns null if no projections available.

getBounds()

async getBounds(name: string): Promise<{
  min: number[];
  max: number[];
}>

Returns projection bounds.

Examples

const bounds = await reader.projections.getBounds("UMAP");

console.log(`X: ${bounds.min[0]} ~ ${bounds.max[0]}`);
console.log(`Y: ${bounds.min[1]} ~ ${bounds.max[1]}`);

clearCache()

clearCache(): void

Clears cached data.

Projection Class

Returned by read() / readDefault().

Properties

readonly name: string; // e.g. "UMAP" or producer-supplied display name
readonly key?: string; // Internal projection identifier when present
readonly method?: string; // Producer-supplied algorithm label
readonly dimensions: number; // Number of axes (typically 2)
readonly coordinates: Float64Array[]; // One Float64Array per dimension

method is the upstream string label written by loupeR (see R/hdf5.R:189-199). It is the preferred way to identify the projection's algorithm; ProjectionInfo.Type (integer enum) is @experimental and may be absent.

Methods

getCoordinates()

getCoordinates(cellIndex: number): number[] | null

Returns coordinates for a specific cell.

Examples

const projection = await reader.projections.read("UMAP");

const coords = projection.getCoordinates(0);
if (coords) {
  console.log(`Cell 0: (${coords[0]}, ${coords[1]})`);
}

getBounds()

getBounds(): { min: number[]; max: number[] }

Returns bounds for all dimensions.

Common Projection Types

Name	Description
UMAP	Uniform Manifold Approximation and Projection
t-SNE	t-distributed Stochastic Neighbor Embedding
PCA	Principal Component Analysis