import * as gc from "./gc.js";
import * as utils from "./utils.js";
import * as internal from "./internal/computePerCellQcFilters.js";
import { PerCellRnaQcMetricsResults } from "./perCellRnaQcMetrics.js";
/**
* Wrapper class for the filtering results, produced by {@linkcode computeSuggestRnaQcFilters}.
* @hideconstructor
*/
export class SuggestRnaQcFiltersResults {
#id;
#results;
constructor(id, raw) {
this.#id = id;
this.#results = raw;
}
/**
* @param {object} [options={}] - Optional parameters.
* @param {boolean} [options.copy=true] - Whether to copy the results from the Wasm heap, see {@linkcode possibleCopy}.
* This should be set to `false` or `"view"` to modify entries, e.g., after calling creating an instance with {@linkcode emptySuggestRnaQcFiltersResults}.
*
* @return {Float64Array|Float64WasmArray} Array containing the filtering threshold on the sums for each batch.
*/
sum(options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.sum(), copy);
}
/**
* @param {object} [options={}] - Optional parameters.
* @param {boolean} [options.copy=true] - Whether to copy the results from the Wasm heap, see {@linkcode possibleCopy}.
* This should be set to `false` or `"view"` to modify entries, e.g., after calling creating an instance with {@linkcode emptySuggestRnaQcFiltersResults}.
*
* @return {Float64Array|Float64WasmArray} Array containing the filtering threshold on the number of detected genes for each batch.
*/
detected(options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.detected(), copy);
}
/**
* @param {number} i - Index of the feature subset of interest.
* @param {object} [options={}] - Optional parameters.
* @param {boolean} [options.copy=true] - Whether to copy the results from the Wasm heap, see {@linkcode possibleCopy}.
* This should be set to `false` or `"view"` to modify entries, e.g., after calling creating an instance with {@linkcode emptySuggestRnaQcFiltersResults}.
*
* @return {Float64Array|Float64WasmArray} Array containing the filtering threshold on the proportions for subset `i` in each batch.
*/
subsetProportion(i, options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.subset_proportion(i), copy);
}
/**
* @return {number} Number of feature subsets in this object.
*/
numberOfSubsets() {
return this.#results.num_subsets();
}
/**
* @return {number} Number of blocks in this object.
*/
numberOfBlocks() {
return this.#results.num_blocks();
}
/**
* @return {boolean} Whether blocking was used to compute the thresholds.
*/
isBlocked() {
return this.#results.isBlocked();
}
/**
* @param {PerCellRnaQcMetricsResults} metrics - Per-cell QC metrics, usually computed by {@linkcode perCellRnaQcMetrics}.
* @param {object} [options={}] - Optional parameters.
* @param {?(Int32WasmArray|Array|TypedArray)} [options.block=null] - Array containing the block assignment for each cell in `metrics`.
* This should have length equal to the number of cells and contain all values in `[0, n)` where `n` is the return value of {@linkcode SuggestRnaQcFilters#numberOfBlocks numberOfBlocks}.
* `block` must be supplied if {@linkcode SuggestRnaQcFilters#isBlocked isBlocked} returns true, otherwise it is ignored.
* @param {boolean} [options.asTypedArray=true] - Whether to return a Uint8Array.
* If `false`, a Uint8WasmArray is returned instead.
* @param {?Uint8WasmArray} [options.buffer=null] - Array of length equal to the number of cells in `metrics`, to be used to store the high-quality calls.
*
* @return {Uint8Array|Uint8WasmArray} Array of length equal to the number of cells in `metrics`.
* Each entry is truthy if the corresponding cell is deemed to be of high-quality based on its values in `metrics`.
* If `buffer` is supplied, the function returns `buffer` if `asTypedArray = false`, or a view on `buffer` if `asTypedArray = true`.
*/
filter(metrics, options = {}) {
const { block = null, asTypedArray = true, buffer = null, ...others } = options;
utils.checkOtherOptions(others);
if (!(metrics instanceof PerCellRnaQcMetricsResults)) {
throw new Error("'metrics' should be a PerCellRnaQcMetricsResults object");
}
return internal.applyFilter(this.#results, metrics, block, asTypedArray, buffer);
}
/**
* @return Frees the memory allocated on the Wasm heap for this object.
* This invalidates this object and all references to it.
*/
free() {
if (this.#results !== null) {
gc.release(this.#id);
this.#results = null;
}
return;
}
}
/**
* Define filters based on the per-cell QC metrics computed from an RNA count matrix.
*
* @param {PerCellRnaQcMetricsResults} metrics - Per-cell QC metrics, usually computed by {@linkcode perCellRnaQcMetrics}.
* @param {object} [options={}] - Optional parameters.
* @param {number} [options.numberOfMADs=3] - Number of median absolute deviations to use to define low-quality outliers.
* @param {?(Int32WasmArray|Array|TypedArray)} [options.block=null] - Array containing the block assignment for each cell.
* This should have length equal to the number of cells and contain all values from 0 to `n - 1` at least once, where `n` is the number of blocks.
* This is used to segregate cells in order to compute filters within each block.
* Alternatively, this may be `null`, in which case all cells are assumed to be in the same block.
*
* @return {SuggestRnaQcFiltersResults} Object containing the filtering results.
*/
export function suggestRnaQcFilters(metrics, options = {}) {
const { numberOfMADs = 3, block = null, ...others } = options;
utils.checkOtherOptions(others);
if (!(metrics instanceof PerCellRnaQcMetricsResults)) {
throw new Error("'metrics' should be a PerCellRnaQcMetricsResults object");
}
return internal.computePerCellQcFilters(
metrics,
block,
(x, use_blocks, bptr) => gc.call(
module => module.suggest_rna_qc_filters(x.results, use_blocks, bptr, numberOfMADs),
SuggestRnaQcFiltersResults
)
);
}
/**
* Create an empty {@linkplain SuggestRnaQcFiltersResults} object, to be filled with custom results.
*
* @param {number} numberOfSubsets Number of feature subsets.
* @param {number} numberOfBlocks Number of blocks in the dataset.
*
* @return {SuggestRnaQcFiltersResults} Object with allocated memory to store QC filters, but no actual values.
*/
export function emptySuggestRnaQcFiltersResults(numberOfSubsets, numberOfBlocks) {
return gc.call(
module => new module.SuggestRnaQcFiltersResults(numberOfSubsets, numberOfBlocks),
SuggestRnaQcFiltersResults,
/* filled = */ false
);
}