mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-25 13:28:11 +08:00
* mocks for redux refactor - for discussion * more API design on redux refactor * add new reuqired dependencies for build * change babel target to use modern browser * remove dead code * remove dead code - joy plots * checkpoint on redux refactoring * checkpoint on redux refactoring * fix mistaken rebase conflict resolution * dead code removal; add name to dataframe backmap * rename dataframe to universe * update eslint config to more closely match prettier * lint * more eslint updates to match prettier * additional config to make eslint match prettier * add expression data to Universe/World * remove obsolete reducers * lint fixes * more eslint cleanup * lint * lint * fix but in countAllOnes when dimensions gt 1 * lint; do not display name metadata field * lint; colors refactor * lint; colors refactor * update comments * first cut at regraph and reset * enable object-curly-braces consistent mode * lint, handle regraph with no selection * fix expression scatterplot bugs * fix regression legend display * add expression data cache * remove console logging * reset cell color on regraph/reset * remove obsolete server URLs * rename UniverseV01 to Universe_REST_API_v01 * add additional comments on the varDataCache * merge universe reducer into controls reducer; simplify initialization-related actions * use spread operator * fix erroneous comment * convert universe and world state to plain objects, and functionalize supporting code (remove ES6 classes) * use spread operator * lint * improve variable names * rename obsCrossfilter to crossfilter and obsDimensionMap to dimensionMap * rename controls2 to controls
This commit is contained in:
Bruce Martin
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// jshint esversion: 6
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import _ from "lodash";
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import * as kvCache from "./keyvalcache";
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/*
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World is a subset of universe. Most code should use world, and should
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(generally) not use Universe. World contains any per-obs or per-var data
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that must be consisstent acorss the app when we view/manipulate subsets
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of Universe.
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Private API indicated by leading underscore in key name (eg, _foo). Anything else
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is public.
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World contains several public keys, obsAnnotations, and obsLayout, which are
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arrays contianing information about an OBS in the same order/offset. In
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other words, world.obsAnnotations[0] and world.obsLayout.X[0] refer to the same
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obs/cell.
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* obsAnnotations:
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obsAnnotations will return an array of objects. Each object contains all annotation
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values for a given observation/cell, keyed by annotation name, PLUS a key
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'__cellId__', containing a REST API ID for this obs/cell (referred to as the
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obsIndex in the REST 0.2 spec or cellIndex in the 0.1 spec.
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Example: [ { __cellId__: 99, cluster: 'blue', numReads: 93933 } ]
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NOTE: world.obsAnnotation should be identical to the old state.cells value,
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EXCEPT that
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* __cellIndex__ renamed to __obsIndex__
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* __x__ and __y__ are now in world.obsLayout
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* __color__ and __colorRBG__ should be moved to controls reducer
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* obsLayout:
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obsLayout will return an object containing two arrays, containing X and Y
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coordinates respectively.
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Example: { X: [ 0.33, 0.23, ... ], Y: [ 0.8, 0.777, ... ]}
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* crossfilter - a crossfilter object across world.obsAnnotations
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* dimensionMap - an object mapping annotation names to dimensions on
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the crossfilter
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*/
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/*
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Summary information for each annotation, keyed by annotation name.
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Value will be an object, containing either 'range' or 'options' object,
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depending on the annotation schema type (categorical or continuous).
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Summarize for BOTH obs and var annotations. Result format:
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{
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obs: {
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annotation_name: { ... },
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...
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},
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var: {
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annotation_name: { ... },
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...
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}
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}
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Example:
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{
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"Splice_sites_Annotated": {
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"range": {
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"min": 26,
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"max": 1075869
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}
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},
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"Selection": {
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"options": {
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"Astrocytes(HEPACAM)": 714,
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"Endothelial(BSC)": 123,
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"Oligodendrocytes(GC)": 294,
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"Neurons(Thy1)": 685,
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"Microglia(CD45)": 1108,
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"Unpanned": 665
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}
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}
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}
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*/
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function summarizeAnnotations(schema, obsAnnotations) {
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/*
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Build and return obs/var summary using any annotation in the schema
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*/
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const obsSummary = _(schema.annotations.obs)
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.keyBy("name")
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.mapValues(anno => {
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const { name, type } = anno;
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const continuous = type === "int32" || type === "float32";
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if (!continuous) {
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return {
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options: _.countBy(obsAnnotations, name)
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};
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}
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if (continuous) {
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let min = Number.POSITIVE_INFINITY;
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let max = Number.NEGATIVE_INFINITY;
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_.forEach(obsAnnotations, obs => {
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const val = Number(obs[name]);
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min = val < min ? val : min;
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max = val > max ? val : max;
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});
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return { range: { min, max } };
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}
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throw new Error("incomprehensible schema");
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})
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.value();
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const varSummary = {}; // TODO XXX - not currently used, so skip it
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return {
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obs: obsSummary,
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var: varSummary
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};
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}
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function templateWorld() {
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const VarDataCacheLowWatermark = 32;
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const VarDataCacheTTLMs = 1000;
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return {
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// map from universe obsIndex to world offset.
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// Undefined / null indicates identity mapping.
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worldObsIndex: null,
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/* schema/version related */
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api: null,
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schema: null,
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nObs: 0,
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nVar: 0,
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/* annotations */
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obsAnnotations: null,
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varAnnotations: null,
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/* layout of graph */
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obsLayout: null,
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/* derived data summaries XXX: consider exploding in place */
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summary: null,
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varDataCache: kvCache.create(
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VarDataCacheLowWatermark,
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VarDataCacheTTLMs
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) /* cache of var data (expression) */
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};
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}
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export function createWorldFromEntireUniverse(universe) {
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if (!universe.finalized) {
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throw new Error("World can't be created from an partial Universe");
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}
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const world = templateWorld();
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// map from the universe obsIndex to our world offset.
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// undefined/null indicates identity map.
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world.worldObsIndex = null;
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/*
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public interface follows
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*/
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/* Schema related */
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world.api = universe.api;
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world.schema = universe.schema;
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world.nObs = universe.nObs;
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world.nVar = universe.nVar;
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/* annotations */
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world.obsAnnotations = universe.obsAnnotations;
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world.varAnnotations = universe.varAnnotations;
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/* layout and display characteristics */
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world.obsLayout = universe.obsLayout;
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/* derived data & summaries */
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world.summary = summarizeAnnotations(world.schema, world.obsAnnotations);
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return world;
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}
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export function createWorldFromCurrentSelection(universe, world, crossfilter) {
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const newWorld = templateWorld();
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/* these don't change as only OBS are selected in our current implementation */
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newWorld.api = world.api;
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newWorld.nVar = world.nVar;
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newWorld.schema = world.schema;
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newWorld.varAnnotations = world.varAnnotations;
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/*
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Subset world from universe based upon world's current selection. Only those
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fields which are subset by observation selection/filtering need to be updated.
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*/
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const numSelected = crossfilter.countFiltered();
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/*
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Create a world which is based upon current selection
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*/
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newWorld.nObs = numSelected;
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newWorld.obsAnnotations = new Array(numSelected);
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newWorld.obsLayout = {
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X: new Array(numSelected),
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Y: new Array(numSelected)
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};
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newWorld.worldObsIndex = new Array(universe.nObs);
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for (let i = 0, sel = 0; i < world.nObs; i += 1) {
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if (crossfilter.isElementFiltered(i)) {
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newWorld.obsAnnotations[sel] = world.obsAnnotations[i];
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newWorld.obsLayout.X[sel] = world.obsLayout.X[i];
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newWorld.obsLayout.Y[sel] = world.obsLayout.Y[i];
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sel += 1;
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}
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}
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// build index to our world offset
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newWorld.worldObsIndex.fill(-1); // default - aka unused
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for (let i = 0; i < newWorld.nObs; i += 1) {
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newWorld.worldObsIndex[newWorld.obsAnnotations[i].__obsIndex__] = i;
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}
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newWorld.summary = summarizeAnnotations(
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newWorld.schema,
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newWorld.obsAnnotations
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);
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return newWorld;
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}
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/*
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Deduce the correct crossfilter dimension type from a metadata
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schema description.
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*/
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function deduceDimensionType(attributes, fieldName) {
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let dimensionType;
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if (attributes.type === "string") {
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dimensionType = "enum";
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} else if (attributes.type === "int32") {
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dimensionType = Int32Array;
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} else if (attributes.type === "float32") {
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dimensionType = Float32Array;
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} else {
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/*
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Currently not supporting boolean and categorical types.
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*/
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console.error(
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`Warning - REST API returned unknown metadata schema (${
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attributes.type
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}) for field ${fieldName}.`
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);
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// skip it - we don't know what to do with this type
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}
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return dimensionType;
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}
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export function createObsDimensionMap(crossfilter, world) {
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/*
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create and return a crossfilter dimension for every obs annotation
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for which we have a supported type.
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*/
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const { schema, obsLayout, worldObsIndex } = world;
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const dimensionMap = _.transform(
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schema.annotations.obs,
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(result, anno) => {
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const dimType = deduceDimensionType(anno, anno.name);
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if (dimType) {
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result[anno.name] = crossfilter.dimension(r => r[anno.name], dimType);
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} // else ignore the annotation
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},
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{}
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);
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/*
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Add crossfilter dimensions allowing filtering on layout
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*/
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const worldIndex = worldObsIndex ? idx => worldObsIndex[idx] : idx => idx;
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dimensionMap.x = crossfilter.dimension(
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r => obsLayout.X[worldIndex(r.__obsIndex__)],
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Float32Array
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);
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dimensionMap.y = crossfilter.dimension(
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r => obsLayout.Y[worldIndex(r.__obsIndex__)],
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Float32Array
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);
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return dimensionMap;
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}
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function worldEqUniverse(world, universe) {
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return world.obsAnnotations === universe.obsAnnotations;
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}
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export function subsetVarData(world, universe, varData) {
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// If world === universe, just return the entire varData array
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if (worldEqUniverse(world, universe)) {
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return varData;
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}
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const newVarData = new Float32Array(world.nObs);
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for (let i = 0; i < world.nObs; i += 1) {
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newVarData[i] = varData[world.obsAnnotations[i].__obsIndex__];
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}
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return newVarData;
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}
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