chihaya v2.0.0

Read delayed matrices in Javascript

Overview

This package provides (incomplete) support for reading chihaya-formatted delayed matrices into Javascript. We do so by creating a ScranMatrix with delayed operations from the tatami library. The resulting matrix can then be used for row- or column-level queries in Javascript or into other scran.js functions. This enables web applications to read delayed matrices generated elsewhere, e.g., via the R interface for saving DelayedArray.

Quick start

Usage is fairly simple once the HDF5 file is available. On browsers, the HDF5 file should be saved to the virtual filesystem using scran.writeFile().

import * as scran from "scran.js";
import * as chihaya from "chihaya";
await scran.initialize(); // may need localFile: true for old Node.js versions.
let mat = await chihaya.load(path_to_file, name_of_group);

The load() function produces a ScranMatrix that can be queried or used in scran.js functions:

let ncols = mat.numberOfColumns();
let first_row = mat.row(0);
let normed = scran.logNormCounts(mat);

See the reference documentation for more details.

Supported operations

Support for the chihaya specification is not yet complete, so only a subset of delayed operations are recognized:

• Unary arithmetic (i.e., where only one of the operands is a delayed matrix)
• Some of the unary math - log, exp, log1p, sqrt, abs and round.
• Combining by row, column
• Subsetting by row, column
• Transposition
• Dimnames assignment (which is silently ignored)

Similarly, only a subset of arrays are supported:

• Dense arrays in non-native storage
• Compressed sparse column matrices

Application developers can add custom handlers for their own delayed operations/arrays through the registerArrayHandler() and registerOperationHandler() functions.

Developer notes

For testing purposes, this package compiles the chihaya C++ library to WebAssembly. Building the Wasm binary requires the Emscripten toolchain and a recent version of CMake. (See also the chihaya.js-docker repository for a pre-built Docker image.) Once these are installed, we can simply do:

cd wasm && ./build.sh 

Testing usually involves some combination of Node flags to enable Wasm support, see the package.json for more details.