mirror of
https://github.com/chanzuckerberg/cellxgene.git
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improve type handling for non-string annotation data (#465)
* improve type handling for non-string annotation data * improve clarity of code
This commit is contained in:
Bruce Martin
committed by
Charlotte Weaver
Charlotte Weaver
parent
2b5094665f
commit
138d30909a
Vendored
+151
-55
@@ -12,34 +12,109 @@ import {
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diffexpDimensionName,
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makeContinuousDimensionName
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} from "../util/nameCreators";
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import { fillRange } from "../util/typedCrossfilter/util";
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function createCategoricalAsBooleansMap(world) {
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/*
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Selection state for categoricals are tracked in an Object that
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has two main components for each category:
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1. mapping of option value to an index
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2. array of bool selection state by index
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Remember that option values can be ANY js type, except undefined/null.
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{
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_category_name_1: {
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// map of option value to index
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optionIndex: Map([
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optval1: index,
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...
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])
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// index->selection true/false state
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optionSelected: [ true/false, true/false, ... ]
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// number of options
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numOptions: number,
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// isTruncated - true if the options for selection has
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// been truncated (ie, was too large to implement)
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}
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}
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*/
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function topNoptions(summary) {
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const counts = _.map(summary.categories, cat => summary.options[cat]);
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const sortIndex = fillRange(new Array(summary.numOptions)).sort(
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(a, b) => counts[b] - counts[a]
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);
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const sortedCategories = _.map(sortIndex, i => summary.categories[i]);
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const sortedCounts = _.map(sortIndex, i => counts[i]);
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const N = globals.maxCategoricalOptionsToDisplay;
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if (sortedCategories.length < N) {
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return [sortedCategories, sortedCounts];
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}
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return [sortedCategories.slice(0, N), sortedCounts.slice(0, N)];
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}
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function createCategoricalSelectionState(state, world) {
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const res = {};
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_.each(world.summary.obs, (value, key) => {
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if (value.options && key !== "name") {
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const optionsAsBooleans = {};
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_.each(value.options, (_value, _key) => {
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optionsAsBooleans[_key] = true;
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});
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res[key] = optionsAsBooleans;
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_.forEach(world.summary.obs, (value, key) => {
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if (value.categories) {
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const isColorField = key.includes("color") || key.includes("Color");
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const isSelectableCategory =
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!isColorField &&
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key !== "name" &&
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value.categories.length < state.maxCategoryItems;
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if (isSelectableCategory) {
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const [optionValue, optionCount] = topNoptions(value);
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// const optionCount = Object.values(value.options);
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const optionIndex = new Map(optionValue.map((v, i) => [v, i]));
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const numOptions = optionIndex.size;
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const optionSelected = new Array(numOptions).fill(true);
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const isTruncated = optionValue.length < value.numOptions;
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res[key] = {
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optionValue, // array: of natively typed option values
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optionIndex, // map: option value (native type) -> option index
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optionSelected, // array: t/f selection state
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numOptions, // number: of options
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isTruncated, // bool: true if list was truncated
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optionCount // array: cardinality of each option
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};
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}
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}
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});
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return res;
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}
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/*
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given a categoricalSelectionState, return the list of all option values
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where selection state is true (ie, they are selected).
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*/
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function selectedValuesForCategory(categorySelectionState) {
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const selectedValues = _([...categorySelectionState.optionIndex])
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.filter(tuple => categorySelectionState.optionSelected[tuple[1]])
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.map(tuple => tuple[0])
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.value();
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return selectedValues;
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}
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const Controls = (
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state = {
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// data loading flag
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loading: false,
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error: null,
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// configuration
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maxCategoryItems: globals.configDefaults.parameters["max-category-items"],
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// the whole big bang
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universe: null,
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// all of the data + selection state
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world: null,
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colorName: null,
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colorRGB: null,
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categoricalAsBooleansMap: null,
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categoricalSelectionState: null,
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crossfilter: null,
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dimensionMap: null,
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userDefinedGenes: [],
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@@ -72,6 +147,17 @@ const Controls = (
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Initialization, World/Universe management
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and data loading.
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******************************************************/
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case "configuration load complete": {
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// there are a couple of configuration items we need to retain
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return {
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...state,
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maxCategoryItems: _.get(
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state.config,
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"parameters.max-category-items",
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globals.configDefaults.parameters["max-category-items"]
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)
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};
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}
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case "initial data load start": {
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return { ...state, loading: true };
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}
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@@ -83,7 +169,10 @@ const Controls = (
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const world = World.createWorldFromEntireUniverse(universe);
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const colorName = new Array(universe.nObs).fill(globals.defaultCellColor);
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const colorRGB = _.map(colorName, c => parseRGB(c));
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const categoricalAsBooleansMap = createCategoricalAsBooleansMap(world);
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const categoricalSelectionState = createCategoricalSelectionState(
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state,
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world
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);
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const crossfilter = Crossfilter(world.obsAnnotations);
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const dimensionMap = World.createObsDimensionMap(crossfilter, world);
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@@ -135,7 +224,7 @@ const Controls = (
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world,
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colorName,
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colorRGB,
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categoricalAsBooleansMap,
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categoricalSelectionState,
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crossfilter,
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dimensionMap,
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colorAccessor: null
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@@ -152,7 +241,10 @@ const Controls = (
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);
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const colorName = new Array(world.nObs).fill(globals.defaultCellColor);
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const colorRGB = _.map(colorName, c => parseRGB(c));
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const categoricalAsBooleansMap = createCategoricalAsBooleansMap(world);
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const categoricalSelectionState = createCategoricalSelectionState(
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state,
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world
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);
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const crossfilter = Crossfilter(world.obsAnnotations);
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const dimensionMap = World.createObsDimensionMap(crossfilter, world);
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@@ -197,7 +289,7 @@ const Controls = (
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world,
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colorName,
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colorRGB,
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categoricalAsBooleansMap,
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categoricalSelectionState,
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crossfilter,
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dimensionMap,
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colorAccessor: null
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@@ -422,83 +514,87 @@ const Controls = (
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Categorical metadata
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*******************************/
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case "categorical metadata filter select": {
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const newCategoricalAsBooleansMap = {
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...state.categoricalAsBooleansMap,
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const newOptionSelected = Array.from(
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state.categoricalSelectionState[action.metadataField].optionSelected
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);
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newOptionSelected[action.optionIndex] = true;
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const newCategoricalSelectionState = {
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...state.categoricalSelectionState,
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[action.metadataField]: {
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...state.categoricalAsBooleansMap[action.metadataField],
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[action.value]: true
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...state.categoricalSelectionState[action.metadataField],
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optionSelected: newOptionSelected
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}
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};
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// update the filter for the one category that changed state
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// update the filter to match all selected options
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const cat = newCategoricalSelectionState[action.metadataField];
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state.dimensionMap[obsAnnoDimensionName(action.metadataField)].filterEnum(
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_.filter(
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_.map(
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newCategoricalAsBooleansMap[action.metadataField],
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(val, key) => (val ? key : false)
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)
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)
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selectedValuesForCategory(cat)
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);
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return {
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...state,
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categoricalAsBooleansMap: newCategoricalAsBooleansMap
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categoricalSelectionState: newCategoricalSelectionState
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};
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}
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case "categorical metadata filter deselect": {
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const newCategoricalAsBooleansMap = {
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...state.categoricalAsBooleansMap,
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const newOptionSelected = Array.from(
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state.categoricalSelectionState[action.metadataField].optionSelected
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);
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newOptionSelected[action.optionIndex] = false;
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const newCategoricalSelectionState = {
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...state.categoricalSelectionState,
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[action.metadataField]: {
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...state.categoricalAsBooleansMap[action.metadataField],
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[action.value]: false
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...state.categoricalSelectionState[action.metadataField],
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optionSelected: newOptionSelected
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}
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};
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// update the filter for the one category that changed state
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// update the filter to match all selected options
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const cat = newCategoricalSelectionState[action.metadataField];
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state.dimensionMap[obsAnnoDimensionName(action.metadataField)].filterEnum(
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_.filter(
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_.map(
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newCategoricalAsBooleansMap[action.metadataField],
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(val, key) => (val ? key : false)
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)
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)
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selectedValuesForCategory(cat)
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);
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return {
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...state,
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categoricalAsBooleansMap: newCategoricalAsBooleansMap
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categoricalSelectionState: newCategoricalSelectionState
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};
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}
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case "categorical metadata filter none of these": {
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const newCategoricalAsBooleansMap = {
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...state.categoricalAsBooleansMap
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};
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_.forEach(
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newCategoricalAsBooleansMap[action.metadataField],
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(v, k, c) => {
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c[k] = false;
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const newCategoricalSelectionState = {
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...state.categoricalSelectionState,
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[action.metadataField]: {
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...state.categoricalSelectionState[action.metadataField],
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optionSelected: Array.from(
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state.categoricalSelectionState[action.metadataField].optionSelected
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).fill(false)
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}
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);
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};
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state.dimensionMap[
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obsAnnoDimensionName(action.metadataField)
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].filterNone();
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return {
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...state,
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categoricalAsBooleansMap: newCategoricalAsBooleansMap
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categoricalSelectionState: newCategoricalSelectionState
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};
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}
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case "categorical metadata filter all of these": {
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const newCategoricalAsBooleansMap = {
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...state.categoricalAsBooleansMap
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};
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_.forEach(
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newCategoricalAsBooleansMap[action.metadataField],
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(v, k, c) => {
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c[k] = true;
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const newCategoricalSelectionState = {
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...state.categoricalSelectionState,
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[action.metadataField]: {
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...state.categoricalSelectionState[action.metadataField],
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optionSelected: Array.from(
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state.categoricalSelectionState[action.metadataField].optionSelected
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).fill(true)
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}
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);
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};
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state.dimensionMap[
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obsAnnoDimensionName(action.metadataField)
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].filterAll();
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return {
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...state,
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categoricalAsBooleansMap: newCategoricalAsBooleansMap
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categoricalSelectionState: newCategoricalSelectionState
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};
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}
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