mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-05 00:48:12 +08:00
Undo/redo (#659)
* immutable crossfilter * first cut at reducer refactor with cascade model * add initial redo/undo implementation * small optimization * integrate expression with history * add tests for new reducers and fix a couple of small initialization bugs * treat tiny lasso selections as a clear * better function name for clarity * fix undo for differential expression * remove logging * fix regression due to bad merge * cleanup and comments for clarity * improve undoable configuration for flexibility * fix stale comments * remove debugging code from production build * rename categoricalSelectionState * rename file * improve comments
This commit is contained in:
Bruce Martin
@@ -0,0 +1,44 @@
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export default function cascadeReducers(arg) {
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/*
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Combined a set of cascading reducers into a single reducer. Cascading
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reducers are reducers which may rely on state computed by another reducer.
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Therefore, they:
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- must be composed in a particular order (currently, this is a simple
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linear list of reducers, run in list order)
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- must have access to partially updated "next state" so they can further
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derive state.
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Parameter is one of:
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- a Map object
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- an array of tuples, [ [key1, reducer1], [key2, reducer2], ... ]
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Ie, cascadeReducers([ ["a", reduceA], ["b", reduceB] ])
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Each reducer will be called with the sigature:
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(prevState, action, sharedNextState, sharedPrevState) => newState
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cascadeReducers will build a composite newState object, much
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like combinedReducers. Additional semantics:
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- reducers guaranteed to be called in order
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- each reducer will receive shared objects
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*/
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const reducers = arg instanceof Map ? arg : new Map(arg);
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const reducerKeys = [...reducers.keys()];
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return (prevState, action) => {
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const nextState = {};
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let stateChange = false;
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for (let i = 0, l = reducerKeys.length; i < l; i += 1) {
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const key = reducerKeys[i];
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const reducer = reducers.get(key);
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const prevStateForKey = prevState ? prevState[key] : undefined;
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const nextStateForKey = reducer(
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prevStateForKey,
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action,
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nextState,
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prevState
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);
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nextState[key] = nextStateForKey;
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stateChange = stateChange || nextStateForKey !== prevStateForKey;
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}
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return stateChange ? nextState : prevState;
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};
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}
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@@ -0,0 +1,105 @@
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import _ from "lodash";
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import { ControlsHelpers } from "../util/stateManager";
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import * as globals from "../globals";
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function maxCategoryItems(state) {
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return _.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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const CategoricalSelection = (
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state,
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action,
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nextSharedState,
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prevSharedState
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) => {
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switch (action.type) {
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case "initial data load complete (universe exists)":
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case "set World to current selection":
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case "reset World to eq Universe": {
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const { world } = nextSharedState;
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return ControlsHelpers.createCategoricalSelection(
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maxCategoryItems(prevSharedState),
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world
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);
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}
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case "categorical metadata filter select": {
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/*
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Set the specific category in this field to false
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*/
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const newCategorySelected = Array.from(
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state[action.metadataField].categorySelected
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);
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newCategorySelected[action.categoryIndex] = true;
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const newCategoricalSelection = {
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...state,
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[action.metadataField]: {
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...state[action.metadataField],
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categorySelected: newCategorySelected
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}
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};
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return newCategoricalSelection;
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}
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case "categorical metadata filter deselect": {
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/*
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Set the specific category in this field to false
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*/
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const newCategorySelected = Array.from(
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state[action.metadataField].categorySelected
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);
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newCategorySelected[action.categoryIndex] = false;
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const newCategoricalSelection = {
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...state,
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[action.metadataField]: {
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...state[action.metadataField],
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categorySelected: newCategorySelected
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}
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};
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return newCategoricalSelection;
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}
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case "categorical metadata filter none of these": {
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/*
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set all categories in this field to false.
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*/
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const newCategoricalSelection = {
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...state,
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[action.metadataField]: {
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...state[action.metadataField],
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categorySelected: Array.from(
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state[action.metadataField].categorySelected
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).fill(false)
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}
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};
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return newCategoricalSelection;
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}
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case "categorical metadata filter all of these": {
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/*
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set all categories in this field to true.
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*/
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const newCategoricalSelection = {
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...state,
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[action.metadataField]: {
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...state[action.metadataField],
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categorySelected: Array.from(
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state[action.metadataField].categorySelected
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).fill(true)
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}
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};
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return newCategoricalSelection;
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}
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default: {
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return state;
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}
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}
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};
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export default CategoricalSelection;
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@@ -0,0 +1,88 @@
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import { createColors } from "../util/stateManager";
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const ColorsReducer = (
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state = {
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colorMode: null,
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colorAccessor: null,
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rgb: null,
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scale: null
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},
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action,
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nextSharedState,
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prevSharedState
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) => {
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switch (action.type) {
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case "initial data load complete (universe exists)":
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case "reset World to eq Universe": {
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const { world } = nextSharedState;
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const colorMode = null;
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const colorAccessor = null;
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const { rgb, scale } = createColors(world, colorMode);
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return {
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...state,
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colorAccessor,
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colorMode,
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rgb,
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scale
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};
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}
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case "set World to current selection": {
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const { colorMode, colorAccessor } = state;
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const { world } = nextSharedState;
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const { rgb, scale } = createColors(world, colorMode, colorAccessor);
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return {
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...state,
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rgb,
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scale
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};
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}
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case "reset colorscale": {
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const { world } = prevSharedState;
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const { rgb, scale } = createColors(world);
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return {
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...state,
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colorMode: null,
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colorAccessor: null,
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rgb,
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scale
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};
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}
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case "color by categorical metadata":
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case "color by continuous metadata": {
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const { world } = prevSharedState;
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const { rgb, scale } = createColors(
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world,
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action.type,
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action.colorAccessor
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);
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return {
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...state,
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colorMode: action.type,
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colorAccessor: action.colorAccessor,
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rgb,
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scale
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};
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}
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case "color by expression": {
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const { world } = prevSharedState;
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const { rgb, scale } = createColors(world, action.type, action.gene);
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return {
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...state,
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colorMode: action.type,
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colorAccessor: action.gene,
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rgb,
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scale
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};
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}
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default: {
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return state;
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}
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}
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};
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export default ColorsReducer;
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Vendored
+10
-439
@@ -2,21 +2,7 @@
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import _ from "lodash";
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import {
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World,
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WorldUtil,
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ControlsHelpers,
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createColors
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} from "../util/stateManager";
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import Crossfilter from "../util/typedCrossfilter";
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import * as globals from "../globals";
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import {
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layoutDimensionName,
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obsAnnoDimensionName,
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userDefinedDimensionName,
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diffexpDimensionName,
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makeContinuousDimensionName
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} from "../util/nameCreators";
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import { WorldUtil } from "../util/stateManager";
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const Controls = (
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state = {
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@@ -24,39 +10,23 @@ const Controls = (
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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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fullUniverseCache: null,
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// all of the data + selection state
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world: null,
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categoricalSelectionState: null,
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crossfilter: null,
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userDefinedGenes: [],
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userDefinedGenesLoading: false,
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diffexpGenes: [],
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// graph color-by
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colorMode: null,
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colorAccessor: null,
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colors: {},
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resettingInterface: false,
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opacityForDeselectedCells: 0.2,
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graphBrushSelection: null,
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continuousSelection: null,
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scatterplotXXaccessor: null, // just easier to read
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scatterplotYYaccessor: null,
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axesHaveBeenDrawn: false,
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graphRenderCounter: 0 /* integer as <Component key={graphRenderCounter} - a change in key forces a remount */,
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__storedStateForCelllist1__: null /* will need procedural control of brush ie., brush.extent https://bl.ocks.org/micahstubbs/3cda05ca68cba260cb81 */,
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__storedStateForCelllist2__: null
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},
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action
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action,
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nextSharedState,
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prevSharedState
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) => {
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/*
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For now, log anything looking like an error to the console.
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@@ -70,190 +40,32 @@ 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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case "initial data load complete (universe exists)": {
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/* first light - create world & other data-driven defaults */
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const { universe } = action;
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const world = World.createWorldFromEntireUniverse(universe);
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const colorMode = null;
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const colors = createColors(world, colorMode);
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const categoricalSelectionState = ControlsHelpers.createCategoricalSelectionState(
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state,
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world
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);
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const crossfilter = World.createObsDimensions(
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new Crossfilter(world.obsAnnotations),
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world
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);
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WorldUtil.clearCaches();
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return {
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...state,
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loading: false,
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error: null,
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universe,
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fullUniverseCache: { world, crossfilter },
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world,
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categoricalSelectionState,
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crossfilter,
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colorMode,
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colorAccessor: null,
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colors,
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resettingInterface: false
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};
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}
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case "reset World to eq Universe": {
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/*
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1. Reset world & crossfilter, using previously created objects which were
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stashed in `fullUniverseCache`
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2. Add crossfilter dimension for all userDefined and diffexp genes/varData,
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as they are not part of the cached crossfilter.
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3. Compute categorical selection summary
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4. Reset all WorldUtil caches
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5. Reset color-by
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*/
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const { userDefinedGenes, diffexpGenes, fullUniverseCache } = state;
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const { world } = fullUniverseCache;
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const crossfilter = ControlsHelpers.createGeneDimensions(
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userDefinedGenes,
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diffexpGenes,
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world,
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fullUniverseCache.crossfilter
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);
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const colorMode = null;
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const colors = createColors(world, colorMode);
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const categoricalSelectionState = ControlsHelpers.createCategoricalSelectionState(
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state,
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world
|
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);
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WorldUtil.clearCaches();
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return {
|
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...state,
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world,
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categoricalSelectionState,
|
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crossfilter,
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colorMode,
|
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colorAccessor: null,
|
||||
colors,
|
||||
resettingInterface: false
|
||||
};
|
||||
}
|
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case "set World to current selection": {
|
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const {
|
||||
userDefinedGenes,
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diffexpGenes,
|
||||
colorMode,
|
||||
colorAccessor
|
||||
} = state;
|
||||
|
||||
/* Set viewable world to be the currently selected data */
|
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const world = World.createWorldFromCurrentSelection(
|
||||
action.universe,
|
||||
action.world,
|
||||
action.crossfilter
|
||||
);
|
||||
const colors = createColors(world, colorMode, colorAccessor);
|
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const categoricalSelectionState = ControlsHelpers.createCategoricalSelectionState(
|
||||
state,
|
||||
world
|
||||
);
|
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let crossfilter = new Crossfilter(world.obsAnnotations);
|
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crossfilter = World.createObsDimensions(crossfilter, world);
|
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crossfilter = ControlsHelpers.createGeneDimensions(
|
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userDefinedGenes,
|
||||
diffexpGenes,
|
||||
world,
|
||||
crossfilter
|
||||
);
|
||||
|
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WorldUtil.clearCaches();
|
||||
|
||||
return {
|
||||
...state,
|
||||
loading: false,
|
||||
error: null,
|
||||
world,
|
||||
colors,
|
||||
categoricalSelectionState,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
case "expression load success": {
|
||||
const { world, universe } = state;
|
||||
let universeVarData = universe.varData;
|
||||
let worldVarData = world.varData;
|
||||
|
||||
// Load new expression data into the varData dataframes, if
|
||||
// not already present.
|
||||
_.forEach(action.expressionData, (val, key) => {
|
||||
// If not already in universe.varData, save entire expression column
|
||||
if (!universeVarData.hasCol(key)) {
|
||||
universeVarData = universeVarData.withCol(key, val);
|
||||
}
|
||||
|
||||
// If not already in world.varData, save sliced expression column
|
||||
if (!worldVarData.hasCol(key)) {
|
||||
// Slice if world !== universe, else just use whole column.
|
||||
// Use the obsAnnotation index as the cut key, as we keep
|
||||
// all world dataframes in sync.
|
||||
let worldValSlice = val;
|
||||
if (!World.worldEqUniverse(world, universe)) {
|
||||
worldValSlice = universeVarData
|
||||
.subset(world.obsAnnotations.rowIndex.keys(), [key], null)
|
||||
.icol(0)
|
||||
.asArray();
|
||||
}
|
||||
|
||||
// Now build world's varData dataframe
|
||||
worldVarData = worldVarData.withCol(
|
||||
key,
|
||||
worldValSlice,
|
||||
world.obsAnnotations.rowIndex
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
// Prune size of varData "cache" if getting out of hand....
|
||||
const { userDefinedGenes, diffexpGenes } = state;
|
||||
const allTheGenesWeNeed = _.uniq(
|
||||
[].concat(
|
||||
userDefinedGenes,
|
||||
diffexpGenes,
|
||||
Object.keys(action.expressionData)
|
||||
)
|
||||
);
|
||||
universeVarData = ControlsHelpers.pruneVarDataCache(
|
||||
universeVarData,
|
||||
allTheGenesWeNeed
|
||||
);
|
||||
worldVarData = ControlsHelpers.pruneVarDataCache(
|
||||
worldVarData,
|
||||
allTheGenesWeNeed
|
||||
);
|
||||
|
||||
return {
|
||||
...state,
|
||||
universe: {
|
||||
...universe,
|
||||
varData: universeVarData
|
||||
},
|
||||
world: {
|
||||
...world,
|
||||
varData: worldVarData
|
||||
}
|
||||
error: null
|
||||
};
|
||||
}
|
||||
case "request user defined gene started": {
|
||||
@@ -269,108 +81,50 @@ const Controls = (
|
||||
};
|
||||
}
|
||||
case "request user defined gene success": {
|
||||
const { world, crossfilter: oldCrossfilter, userDefinedGenes } = state;
|
||||
const _userDefinedGenes = userDefinedGenes.slice();
|
||||
const gene = action.data.genes[0];
|
||||
|
||||
const crossfilter = oldCrossfilter.addDimension(
|
||||
userDefinedDimensionName(gene),
|
||||
"scalar",
|
||||
world.varData.col(gene).asArray(),
|
||||
Float32Array
|
||||
const { userDefinedGenes } = state;
|
||||
const _userDefinedGenes = _.uniq(
|
||||
userDefinedGenes.concat(action.data.genes)
|
||||
);
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
userDefinedGenes: _userDefinedGenes,
|
||||
userDefinedGenesLoading: false
|
||||
};
|
||||
}
|
||||
case "request differential expression success": {
|
||||
const { world, crossfilter: oldCrossfilter } = state;
|
||||
const { world } = prevSharedState;
|
||||
const _diffexpGenes = [];
|
||||
|
||||
action.data.forEach(d => {
|
||||
_diffexpGenes.push(world.varAnnotations.at(d[0], "name"));
|
||||
});
|
||||
|
||||
let crossfilter = oldCrossfilter;
|
||||
_.forEach(_diffexpGenes, gene => {
|
||||
crossfilter = crossfilter.addDimension(
|
||||
diffexpDimensionName(gene),
|
||||
"scalar",
|
||||
world.varData.col(gene).asArray(),
|
||||
Float32Array
|
||||
);
|
||||
});
|
||||
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
diffexpGenes: _diffexpGenes
|
||||
};
|
||||
}
|
||||
case "clear differential expression": {
|
||||
const { world } = state;
|
||||
let { crossfilter } = state;
|
||||
_.forEach(action.diffExp, values => {
|
||||
const name = world.varAnnotations.at(values[0], "name");
|
||||
crossfilter = crossfilter.delDimension(diffexpDimensionName(name));
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
diffexpGenes: []
|
||||
};
|
||||
}
|
||||
case "user defined gene": {
|
||||
/*
|
||||
this could also live in expression success with a conditional,
|
||||
but that handles diffexp also
|
||||
*/
|
||||
const newUserDefinedGenes = state.userDefinedGenes.slice();
|
||||
newUserDefinedGenes.push(action.data);
|
||||
return {
|
||||
...state,
|
||||
userDefinedGenes: newUserDefinedGenes
|
||||
};
|
||||
}
|
||||
case "clear user defined gene": {
|
||||
const { userDefinedGenes, crossfilter: oldCrossfilter } = state;
|
||||
const { userDefinedGenes } = state;
|
||||
const newUserDefinedGenes = _.filter(
|
||||
userDefinedGenes,
|
||||
d => d !== action.data
|
||||
);
|
||||
const crossfilter = oldCrossfilter.delDimension(
|
||||
userDefinedDimensionName(action.data)
|
||||
);
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
userDefinedGenes: newUserDefinedGenes
|
||||
};
|
||||
}
|
||||
case "clear all user defined genes": {
|
||||
const { userDefinedGenes } = state;
|
||||
let { crossfilter } = state;
|
||||
_.forEach(userDefinedGenes, gene => {
|
||||
crossfilter = crossfilter.delDimension(userDefinedDimensionName(gene));
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
userDefinedGenes: []
|
||||
};
|
||||
}
|
||||
case "reset colorscale": {
|
||||
const { world } = state;
|
||||
return {
|
||||
...state,
|
||||
colorMode: null,
|
||||
colorAccessor: null,
|
||||
colors: createColors(world)
|
||||
};
|
||||
}
|
||||
case "expression load error":
|
||||
case "initial data load error": {
|
||||
return {
|
||||
@@ -383,69 +137,6 @@ const Controls = (
|
||||
/*******************************
|
||||
User Events
|
||||
*******************************/
|
||||
case "graph brush selection change": {
|
||||
const name = layoutDimensionName("XY");
|
||||
const [x0, y0] = action.brushCoords.northwest;
|
||||
const [x1, y1] = action.brushCoords.southeast;
|
||||
const crossfilter = state.crossfilter.select(name, {
|
||||
mode: "within-rect",
|
||||
x0,
|
||||
y0,
|
||||
x1,
|
||||
y1
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
graphBrushSelection: action.brushCoords
|
||||
};
|
||||
}
|
||||
case "lasso deselect":
|
||||
case "graph brush deselect": {
|
||||
const name = layoutDimensionName("XY");
|
||||
const crossfilter = state.crossfilter.select(name, { mode: "all" });
|
||||
return {
|
||||
...state,
|
||||
crossfilter,
|
||||
graphBrushSelection: null
|
||||
};
|
||||
}
|
||||
case "lasso selection": {
|
||||
const { polygon } = action;
|
||||
const name = layoutDimensionName("XY");
|
||||
const { crossfilter: oldCrossfilter } = state;
|
||||
let crossfilter;
|
||||
if (polygon.length < 3) {
|
||||
// single point or a line is not a polygon, and is therefore a deselect
|
||||
crossfilter = oldCrossfilter.select(name, { mode: "all" });
|
||||
} else {
|
||||
crossfilter = oldCrossfilter.select(name, {
|
||||
mode: "within-polygon",
|
||||
polygon
|
||||
});
|
||||
}
|
||||
return {
|
||||
...state,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
case "continuous metadata histogram brush": {
|
||||
const name = makeContinuousDimensionName(
|
||||
action.continuousNamespace,
|
||||
action.selection
|
||||
);
|
||||
let { crossfilter } = state;
|
||||
|
||||
// action.selection: metadata name being selected
|
||||
// action.range: filter range, or null if deselected
|
||||
if (!action.range) {
|
||||
crossfilter = crossfilter.select(name, { mode: "all" });
|
||||
} else {
|
||||
const [lo, hi] = action.range;
|
||||
crossfilter = crossfilter.select(name, { mode: "range", lo, hi });
|
||||
}
|
||||
return { ...state, crossfilter };
|
||||
}
|
||||
case "change opacity deselected cells in 2d graph background":
|
||||
return {
|
||||
...state,
|
||||
@@ -464,126 +155,6 @@ const Controls = (
|
||||
resettingInterface: true
|
||||
};
|
||||
}
|
||||
/*******************************
|
||||
Categorical metadata
|
||||
*******************************/
|
||||
case "categorical metadata filter select": {
|
||||
const newCategorySelected = Array.from(
|
||||
state.categoricalSelectionState[action.metadataField].categorySelected
|
||||
);
|
||||
newCategorySelected[action.categoryIndex] = true;
|
||||
const newCategoricalSelectionState = {
|
||||
...state.categoricalSelectionState,
|
||||
[action.metadataField]: {
|
||||
...state.categoricalSelectionState[action.metadataField],
|
||||
categorySelected: newCategorySelected
|
||||
}
|
||||
};
|
||||
|
||||
// update the filter to match all selected options
|
||||
const cat = newCategoricalSelectionState[action.metadataField];
|
||||
const dName = obsAnnoDimensionName(action.metadataField);
|
||||
const crossfilter = state.crossfilter.select(dName, {
|
||||
mode: "exact",
|
||||
values: ControlsHelpers.selectedValuesForCategory(cat)
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
categoricalSelectionState: newCategoricalSelectionState,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
case "categorical metadata filter deselect": {
|
||||
const newCategorySelected = Array.from(
|
||||
state.categoricalSelectionState[action.metadataField].categorySelected
|
||||
);
|
||||
newCategorySelected[action.categoryIndex] = false;
|
||||
const newCategoricalSelectionState = {
|
||||
...state.categoricalSelectionState,
|
||||
[action.metadataField]: {
|
||||
...state.categoricalSelectionState[action.metadataField],
|
||||
categorySelected: newCategorySelected
|
||||
}
|
||||
};
|
||||
|
||||
// update the filter to match all selected options
|
||||
const cat = newCategoricalSelectionState[action.metadataField];
|
||||
const dName = obsAnnoDimensionName(action.metadataField);
|
||||
const crossfilter = state.crossfilter.select(dName, {
|
||||
mode: "exact",
|
||||
values: ControlsHelpers.selectedValuesForCategory(cat)
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
categoricalSelectionState: newCategoricalSelectionState,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
case "categorical metadata filter none of these": {
|
||||
const newCategoricalSelectionState = {
|
||||
...state.categoricalSelectionState,
|
||||
[action.metadataField]: {
|
||||
...state.categoricalSelectionState[action.metadataField],
|
||||
categorySelected: Array.from(
|
||||
state.categoricalSelectionState[action.metadataField]
|
||||
.categorySelected
|
||||
).fill(false)
|
||||
}
|
||||
};
|
||||
const dName = obsAnnoDimensionName(action.metadataField);
|
||||
const crossfilter = state.crossfilter.select(dName, {
|
||||
mode: "none"
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
categoricalSelectionState: newCategoricalSelectionState,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
case "categorical metadata filter all of these": {
|
||||
const newCategoricalSelectionState = {
|
||||
...state.categoricalSelectionState,
|
||||
[action.metadataField]: {
|
||||
...state.categoricalSelectionState[action.metadataField],
|
||||
categorySelected: Array.from(
|
||||
state.categoricalSelectionState[action.metadataField]
|
||||
.categorySelected
|
||||
).fill(true)
|
||||
}
|
||||
};
|
||||
const dName = obsAnnoDimensionName(action.metadataField);
|
||||
const crossfilter = state.crossfilter.select(dName, {
|
||||
mode: "all"
|
||||
});
|
||||
return {
|
||||
...state,
|
||||
categoricalSelectionState: newCategoricalSelectionState,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
|
||||
/*******************************
|
||||
Color Scale
|
||||
*******************************/
|
||||
case "color by categorical metadata":
|
||||
case "color by continuous metadata": {
|
||||
const { world } = state;
|
||||
return {
|
||||
...state,
|
||||
colorMode: action.type,
|
||||
colorAccessor: action.colorAccessor,
|
||||
colors: createColors(world, action.type, action.colorAccessor)
|
||||
};
|
||||
}
|
||||
case "color by expression": {
|
||||
const { world } = state;
|
||||
return {
|
||||
...state,
|
||||
colorMode: action.type,
|
||||
colorAccessor: action.gene,
|
||||
colors: createColors(world, action.type, action.gene)
|
||||
};
|
||||
}
|
||||
|
||||
/*******************************
|
||||
Scatterplot
|
||||
|
||||
@@ -0,0 +1,189 @@
|
||||
import _ from "lodash";
|
||||
|
||||
import Crossfilter from "../util/typedCrossfilter";
|
||||
import { World, ControlsHelpers } from "../util/stateManager";
|
||||
import {
|
||||
layoutDimensionName,
|
||||
obsAnnoDimensionName,
|
||||
userDefinedDimensionName,
|
||||
diffexpDimensionName,
|
||||
makeContinuousDimensionName
|
||||
} from "../util/nameCreators";
|
||||
|
||||
const CrossfilterReducer = (
|
||||
state = null,
|
||||
action,
|
||||
nextSharedState,
|
||||
prevSharedState
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "initial data load complete (universe exists)": {
|
||||
const { world } = nextSharedState;
|
||||
const crossfilter = World.createObsDimensions(
|
||||
new Crossfilter(world.obsAnnotations),
|
||||
world
|
||||
);
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
case "reset World to eq Universe": {
|
||||
const { userDefinedGenes, diffexpGenes } = prevSharedState.controls;
|
||||
const { world } = nextSharedState;
|
||||
const crossfilter = ControlsHelpers.createGeneDimensions(
|
||||
userDefinedGenes,
|
||||
diffexpGenes,
|
||||
world,
|
||||
prevSharedState.resetCache.crossfilter
|
||||
);
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
case "set World to current selection": {
|
||||
const { userDefinedGenes, diffexpGenes } = prevSharedState.controls;
|
||||
const { world } = nextSharedState;
|
||||
let crossfilter = new Crossfilter(world.obsAnnotations);
|
||||
crossfilter = World.createObsDimensions(crossfilter, world);
|
||||
crossfilter = ControlsHelpers.createGeneDimensions(
|
||||
userDefinedGenes,
|
||||
diffexpGenes,
|
||||
world,
|
||||
crossfilter
|
||||
);
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
case "request user defined gene success": {
|
||||
const { world } = prevSharedState;
|
||||
const gene = action.data.genes[0];
|
||||
return state.addDimension(
|
||||
userDefinedDimensionName(gene),
|
||||
"scalar",
|
||||
world.varData.col(gene).asArray(),
|
||||
Float32Array
|
||||
);
|
||||
}
|
||||
|
||||
case "request differential expression success": {
|
||||
const { world } = prevSharedState;
|
||||
const genes = _.map(action.data, d =>
|
||||
world.varAnnotations.at(d[0], "name")
|
||||
);
|
||||
const crossfilter = _.reduce(
|
||||
genes,
|
||||
(xfltr, gene) =>
|
||||
xfltr.addDimension(
|
||||
diffexpDimensionName(gene),
|
||||
"scalar",
|
||||
world.varData.col(gene).asArray(),
|
||||
Float32Array
|
||||
),
|
||||
state
|
||||
);
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
case "clear differential expression": {
|
||||
const { world } = prevSharedState;
|
||||
const crossfilter = _.reduce(
|
||||
action.diffExp,
|
||||
(xfltr, values) => {
|
||||
const name = world.varAnnotations.at(values[0], "name");
|
||||
return xfltr.delDimension(diffexpDimensionName(name));
|
||||
},
|
||||
state
|
||||
);
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
case "clear user defined gene": {
|
||||
return state.delDimension(userDefinedDimensionName(action.data));
|
||||
}
|
||||
|
||||
case "clear all user defined genes": {
|
||||
const { userDefinedGenes } = prevSharedState.controls;
|
||||
const crossfilter = _.reduce(
|
||||
userDefinedGenes,
|
||||
(xfltr, gene) => xfltr.delDimension(userDefinedDimensionName(gene)),
|
||||
state
|
||||
);
|
||||
return crossfilter;
|
||||
}
|
||||
|
||||
case "graph brush selection change": {
|
||||
const name = layoutDimensionName("XY");
|
||||
const [x0, y0] = action.brushCoords.northwest;
|
||||
const [x1, y1] = action.brushCoords.southeast;
|
||||
return state.select(name, {
|
||||
mode: "within-rect",
|
||||
x0,
|
||||
y0,
|
||||
x1,
|
||||
y1
|
||||
});
|
||||
}
|
||||
|
||||
case "lasso deselect":
|
||||
case "graph brush deselect": {
|
||||
const name = layoutDimensionName("XY");
|
||||
return state.select(name, { mode: "all" });
|
||||
}
|
||||
|
||||
case "lasso selection": {
|
||||
const { polygon } = action;
|
||||
const name = layoutDimensionName("XY");
|
||||
if (polygon.length < 3) {
|
||||
// single point or a line is not a polygon, and is therefore a deselect
|
||||
return state.select(name, { mode: "all" });
|
||||
}
|
||||
return state.select(name, {
|
||||
mode: "within-polygon",
|
||||
polygon
|
||||
});
|
||||
}
|
||||
|
||||
case "continuous metadata histogram start":
|
||||
case "continuous metadata histogram brush":
|
||||
case "continuous metadata histogram end": {
|
||||
const name = makeContinuousDimensionName(
|
||||
action.continuousNamespace,
|
||||
action.selection
|
||||
);
|
||||
// action.selection: metadata name being selected
|
||||
// action.range: filter range, or null if deselected
|
||||
if (!action.range) {
|
||||
return state.select(name, { mode: "all" });
|
||||
}
|
||||
const [lo, hi] = action.range;
|
||||
const newState = state.select(name, { mode: "range", lo, hi });
|
||||
return newState;
|
||||
}
|
||||
|
||||
case "categorical metadata filter select":
|
||||
case "categorical metadata filter deselect": {
|
||||
const { categoricalSelection } = nextSharedState;
|
||||
const cat = categoricalSelection[action.metadataField];
|
||||
return state.select(obsAnnoDimensionName(action.metadataField), {
|
||||
mode: "exact",
|
||||
values: ControlsHelpers.selectedValuesForCategory(cat)
|
||||
});
|
||||
}
|
||||
|
||||
case "categorical metadata filter none of these": {
|
||||
return state.select(obsAnnoDimensionName(action.metadataField), {
|
||||
mode: "none"
|
||||
});
|
||||
}
|
||||
|
||||
case "categorical metadata filter all of these": {
|
||||
return state.select(obsAnnoDimensionName(action.metadataField), {
|
||||
mode: "all"
|
||||
});
|
||||
}
|
||||
|
||||
default: {
|
||||
return state;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
export default CrossfilterReducer;
|
||||
@@ -1,20 +1,86 @@
|
||||
// jshint esversion: 6
|
||||
import { combineReducers, createStore, applyMiddleware } from "redux";
|
||||
import { createStore, applyMiddleware } from "redux";
|
||||
import thunk from "redux-thunk";
|
||||
import { composeWithDevTools } from "redux-devtools-extension";
|
||||
|
||||
import cascadeReducers from "./cascade";
|
||||
import undoable from "./undoable";
|
||||
import config from "./config";
|
||||
import universe from "./universe";
|
||||
import world from "./world";
|
||||
import categoricalSelection from "./categoricalSelection";
|
||||
import crossfilter from "./crossfilter";
|
||||
import colors from "./colors";
|
||||
import differential from "./differential";
|
||||
import responsive from "./responsive";
|
||||
import controls from "./controls";
|
||||
import resetCache from "./resetCache";
|
||||
|
||||
const Reducer = combineReducers({
|
||||
config,
|
||||
responsive,
|
||||
controls,
|
||||
differential
|
||||
});
|
||||
const ignoredActions = new Set([
|
||||
// these actions will not affect history, ie, we will
|
||||
// not snapshot history upon these actions. These take
|
||||
// precedent over `clearHistoryUponActions`
|
||||
"url changed",
|
||||
"interface reset started",
|
||||
"initial data load start",
|
||||
"configuration load complete",
|
||||
"increment graph render counter",
|
||||
"window resize",
|
||||
|
||||
const store = createStore(Reducer, composeWithDevTools(applyMiddleware(thunk)));
|
||||
"lasso started",
|
||||
|
||||
"request differential expression success",
|
||||
|
||||
"expression load start",
|
||||
"expression load success",
|
||||
"expression load error",
|
||||
|
||||
"continuous metadata histogram brush",
|
||||
"continuous metadata histogram end",
|
||||
|
||||
"request user defined gene started",
|
||||
"request user defined gene success",
|
||||
"request user defined gene error",
|
||||
"bulk user defined gene complete",
|
||||
"single user defined gene complete"
|
||||
]);
|
||||
|
||||
const clearOnActions = new Set([
|
||||
// history will be cleared when these actions occur
|
||||
"initial data load complete (universe exists)",
|
||||
"reset World to eq Universe",
|
||||
"initial data load error"
|
||||
]);
|
||||
|
||||
/* configuration for the undoable meta reducer */
|
||||
const undoableConfig = {
|
||||
historyLimit: 50, // maximum history size
|
||||
skipActionFilter: (state, action) => ignoredActions.has(action.type),
|
||||
clearOnActionFilter: (state, action) => clearOnActions.has(action.type)
|
||||
};
|
||||
|
||||
const Reducer = undoable(
|
||||
cascadeReducers([
|
||||
["config", config],
|
||||
["universe", universe],
|
||||
["world", world],
|
||||
["categoricalSelection", categoricalSelection],
|
||||
["crossfilter", crossfilter],
|
||||
["colors", colors],
|
||||
["controls", controls],
|
||||
["differential", differential],
|
||||
["responsive", responsive],
|
||||
["resetCache", resetCache]
|
||||
]),
|
||||
[
|
||||
"world",
|
||||
"categoricalSelection",
|
||||
"crossfilter",
|
||||
"colors",
|
||||
"controls",
|
||||
"differential"
|
||||
],
|
||||
undoableConfig
|
||||
);
|
||||
|
||||
const store = createStore(Reducer, applyMiddleware(thunk));
|
||||
|
||||
export default store;
|
||||
|
||||
@@ -0,0 +1,28 @@
|
||||
/*
|
||||
Reducer which caches derived state to be used in a reset
|
||||
*/
|
||||
|
||||
const ResetCacheReducer = (
|
||||
state = {
|
||||
world: null,
|
||||
crossfilter: null
|
||||
},
|
||||
action,
|
||||
nextSharedState
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "initial data load complete (universe exists)": {
|
||||
const { world, crossfilter } = nextSharedState;
|
||||
return {
|
||||
...state,
|
||||
world,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
default: {
|
||||
return state;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
export default ResetCacheReducer;
|
||||
@@ -0,0 +1,167 @@
|
||||
/*
|
||||
A redo/undo meta reducer for Redux. Designed to work well with the cascadeReducer().
|
||||
|
||||
Requires three parameters:
|
||||
* reducer - a reducer, which MUST return an object as state.
|
||||
* undoableKeys - an array of object keys (strings). If any of these keys
|
||||
are in the object/state returned by the reducer, they will be treated as
|
||||
state to be made "undoable".
|
||||
* options - an optional object, which may contain the following parameters:
|
||||
* historyLimit: max number of historical states to remember (aka max undo depth)
|
||||
* skipActionFilter: filter function, (state, action) => bool. If it returns
|
||||
truthy, the current state will not be pushed onto the history stack.
|
||||
* clearOnActionFilter: filter function, (state, action) => bool. If it returns
|
||||
truthy, the history state will be cleared as part of handling this action.
|
||||
|
||||
skipActionFilter has precedence over clearOnActionFilter.
|
||||
|
||||
This meta reducer accepts three actions types:
|
||||
* @@undoable/undo - move back in history
|
||||
* @@undoable/redo - move forward in history
|
||||
* @@undoable/clear - clear history
|
||||
*/
|
||||
|
||||
const historyKeyPrefix = "@@undoable/";
|
||||
const pastKey = `${historyKeyPrefix}past`;
|
||||
const futureKey = `${historyKeyPrefix}future`;
|
||||
const defaultHistoryLimit = -100;
|
||||
|
||||
const Undoable = (reducer, undoableKeys, options = {}) => {
|
||||
let { historyLimit } = options;
|
||||
if (!historyLimit) historyLimit = defaultHistoryLimit;
|
||||
if (historyLimit > 0) historyLimit = -historyLimit;
|
||||
const skipActionFilter = options.skipActionFilter || (() => false);
|
||||
const clearOnActionFilter = options.clearOnActionFilter || (() => false);
|
||||
|
||||
if (!Array.isArray(undoableKeys) || undoableKeys.length === 0)
|
||||
throw new Error("undoable keys array must be specified");
|
||||
const undoableKeysSet = new Set(undoableKeys);
|
||||
|
||||
function undo(currentState) {
|
||||
const past = currentState[pastKey];
|
||||
const future = currentState[futureKey];
|
||||
if (past.length === 0) return currentState;
|
||||
const currentUndoableState = Object.entries(currentState).filter(kv =>
|
||||
undoableKeysSet.has(kv[0])
|
||||
);
|
||||
const newPast = [...past];
|
||||
const newState = newPast.pop();
|
||||
const newFuture = push(future, currentUndoableState);
|
||||
const nextState = {
|
||||
...currentState,
|
||||
...fromEntries(newState),
|
||||
[pastKey]: newPast,
|
||||
[futureKey]: newFuture
|
||||
};
|
||||
return nextState;
|
||||
}
|
||||
|
||||
function redo(currentState) {
|
||||
const past = currentState[pastKey] || [];
|
||||
const future = currentState[futureKey] || [];
|
||||
if (future.length === 0) return currentState;
|
||||
const currentUndoableState = Object.entries(currentState).filter(kv =>
|
||||
undoableKeysSet.has(kv[0])
|
||||
);
|
||||
const newFuture = [...future];
|
||||
const newState = newFuture.pop();
|
||||
const newPast = push(past, currentUndoableState);
|
||||
const nextState = {
|
||||
...currentState,
|
||||
...fromEntries(newState),
|
||||
[pastKey]: newPast,
|
||||
[futureKey]: newFuture
|
||||
};
|
||||
return nextState;
|
||||
}
|
||||
|
||||
function clear(currentState) {
|
||||
return {
|
||||
...currentState,
|
||||
[pastKey]: [],
|
||||
[futureKey]: []
|
||||
};
|
||||
}
|
||||
|
||||
function skip(currentState, action) {
|
||||
const past = currentState[pastKey] || [];
|
||||
const res = reducer(currentState, action);
|
||||
return {
|
||||
...res,
|
||||
[pastKey]: past,
|
||||
[futureKey]: []
|
||||
};
|
||||
}
|
||||
|
||||
function save(currentState, action) {
|
||||
const past = currentState[pastKey] || [];
|
||||
const currentUndoableState = Object.entries(currentState).filter(kv =>
|
||||
undoableKeysSet.has(kv[0])
|
||||
);
|
||||
const res = reducer(currentState, action);
|
||||
const newPast = push(past, currentUndoableState, historyLimit);
|
||||
const nextState = {
|
||||
...res,
|
||||
[pastKey]: newPast,
|
||||
[futureKey]: []
|
||||
};
|
||||
return nextState;
|
||||
}
|
||||
|
||||
return (
|
||||
currentState = {
|
||||
[pastKey]: [],
|
||||
[futureKey]: []
|
||||
},
|
||||
action
|
||||
) => {
|
||||
const aType = action.type;
|
||||
switch (aType) {
|
||||
case "@@undoable/undo": {
|
||||
return undo(currentState, action);
|
||||
}
|
||||
case "@@undoable/redo": {
|
||||
return redo(currentState, action);
|
||||
}
|
||||
case "@@undoable/clear": {
|
||||
return clear(currentState, action);
|
||||
}
|
||||
default: {
|
||||
if (skipActionFilter(currentState, action)) {
|
||||
return skip(currentState, action);
|
||||
}
|
||||
if (clearOnActionFilter(currentState, action)) {
|
||||
return clear(skip(currentState, action));
|
||||
}
|
||||
return save(currentState, action);
|
||||
}
|
||||
}
|
||||
};
|
||||
};
|
||||
|
||||
function push(arr, val, limit = undefined) {
|
||||
/*
|
||||
functional array push, with a max length limit to the new array.
|
||||
Like Array.push, except it returns new array and discards as needed
|
||||
to enforce the length limit.
|
||||
*/
|
||||
const narr = arr.slice(limit);
|
||||
narr.push(val);
|
||||
return narr;
|
||||
}
|
||||
|
||||
function fromEntries(arr) {
|
||||
/*
|
||||
Similar to Object.fromEntries, but only handles array.
|
||||
This could be replaced with the standard fucnction once it
|
||||
is widely available. As of 3/20/2019, it has not yet
|
||||
been released in the Chrome stable channel.
|
||||
*/
|
||||
const obj = {};
|
||||
for (let i = 0, l = arr.length; i < l; i += 1) {
|
||||
obj[arr[i][0]] = arr[i][1];
|
||||
}
|
||||
return obj;
|
||||
}
|
||||
|
||||
export default Undoable;
|
||||
@@ -0,0 +1,47 @@
|
||||
import _ from "lodash";
|
||||
|
||||
import { ControlsHelpers } from "../util/stateManager";
|
||||
|
||||
const Universe = (state = null, action, nextSharedState, prevSharedState) => {
|
||||
switch (action.type) {
|
||||
case "initial data load complete (universe exists)": {
|
||||
const { universe } = action;
|
||||
return universe;
|
||||
}
|
||||
|
||||
case "expression load success": {
|
||||
let { varData } = state;
|
||||
|
||||
// Load new expression data into the varData dataframes, if
|
||||
// not already present.
|
||||
_.forEach(action.expressionData, (val, key) => {
|
||||
// If not already in universe.varData, save entire expression column
|
||||
if (!varData.hasCol(key)) {
|
||||
varData = varData.withCol(key, val);
|
||||
}
|
||||
});
|
||||
|
||||
// Prune size of varData "cache" if getting out of hand....
|
||||
const { userDefinedGenes, diffexpGenes } = prevSharedState;
|
||||
const allTheGenesWeNeed = _.uniq(
|
||||
[].concat(
|
||||
userDefinedGenes,
|
||||
diffexpGenes,
|
||||
Object.keys(action.expressionData)
|
||||
)
|
||||
);
|
||||
varData = ControlsHelpers.pruneVarDataCache(varData, allTheGenesWeNeed);
|
||||
|
||||
return {
|
||||
...state,
|
||||
varData
|
||||
};
|
||||
}
|
||||
|
||||
default: {
|
||||
return state;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
export default Universe;
|
||||
@@ -0,0 +1,88 @@
|
||||
import _ from "lodash";
|
||||
|
||||
import { World, ControlsHelpers } from "../util/stateManager";
|
||||
|
||||
const WorldReducer = (
|
||||
state = null,
|
||||
action,
|
||||
nextSharedState,
|
||||
prevSharedState
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "initial data load complete (universe exists)": {
|
||||
const { universe } = nextSharedState;
|
||||
const world = World.createWorldFromEntireUniverse(universe);
|
||||
return world;
|
||||
}
|
||||
|
||||
case "reset World to eq Universe": {
|
||||
return prevSharedState.resetCache.world;
|
||||
}
|
||||
|
||||
case "set World to current selection": {
|
||||
/* Set viewable world to be the currently selected data */
|
||||
const world = World.createWorldFromCurrentSelection(
|
||||
action.universe,
|
||||
action.world,
|
||||
action.crossfilter
|
||||
);
|
||||
return world;
|
||||
}
|
||||
|
||||
case "expression load success": {
|
||||
const { universe } = nextSharedState;
|
||||
const universeVarData = universe.varData;
|
||||
let worldVarData = state.varData;
|
||||
|
||||
// Load new expression data into the varData dataframes, if
|
||||
// not already present.
|
||||
_.forEach(action.expressionData, (val, key) => {
|
||||
// If not already in world.varData, save sliced expression column
|
||||
if (!worldVarData.hasCol(key)) {
|
||||
// Slice if world !== universe, else just use whole column.
|
||||
// Use the obsAnnotation index as the cut key, as we keep
|
||||
// all world dataframes in sync.
|
||||
let worldValSlice = val;
|
||||
if (!World.worldEqUniverse(state, universe)) {
|
||||
worldValSlice = universeVarData
|
||||
.subset(state.obsAnnotations.rowIndex.keys(), [key], null)
|
||||
.icol(0)
|
||||
.asArray();
|
||||
}
|
||||
|
||||
// Now build world's varData dataframe
|
||||
worldVarData = worldVarData.withCol(
|
||||
key,
|
||||
worldValSlice,
|
||||
state.obsAnnotations.rowIndex
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
// Prune size of varData "cache" if getting out of hand....
|
||||
const { userDefinedGenes, diffexpGenes } = prevSharedState;
|
||||
const allTheGenesWeNeed = _.uniq(
|
||||
[].concat(
|
||||
userDefinedGenes,
|
||||
diffexpGenes,
|
||||
Object.keys(action.expressionData)
|
||||
)
|
||||
);
|
||||
worldVarData = ControlsHelpers.pruneVarDataCache(
|
||||
worldVarData,
|
||||
allTheGenesWeNeed
|
||||
);
|
||||
|
||||
return {
|
||||
...state,
|
||||
varData: worldVarData
|
||||
};
|
||||
}
|
||||
|
||||
default: {
|
||||
return state;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
export default WorldReducer;
|
||||
Reference in New Issue
Block a user