mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-04 03:08:12 +08:00
Experimental - manual annotations (#837)
* icons, partway * redux for values * onChange * cancel * annotations lifecycle for category names * copy categorical * edit category * add Dataframe.withColsFrom * render user annotations; default add/delete annotation category * add label name to actions * category name edit * error checking improvements * change schema field isUserAnnotation to writable * always have an unassigned label; implement delete label * implement add new label and edit label name * label current cell selection * fix select exact bug in crossfilter * clean up categorical reducer * fix tests * remove debugging printf * implement subset/reset for user annotations * undo redo support for user annotations * remove duplicate button from categories * add modal * remove obsolete duplicate annotation reducers * remove old debugging printf * connect modal to annotation create and dup * initial full-stack wiring * finish up end-to-end wiring * fix existing unit tests * fix pytests to match new schema API * remove debugging printfs * add label file rotation * remove obsolete comment * add fbs encode/decode tests * add tests for writable annotations * simplify code * fix hashing bug with FBS encoding * lint * fix smoke tests * improve error checking in Dataframe.withColsFrom * add unit test for Dataframe.withColsFrom * add unit test for Dataframe.columns and Dataframe.renameCol * fix bug in FBS encode, add better error checks, refactor * add FBS encode/decode test * add clarifying comment * clean up action type names; fix state inconsistency in crossfilter update * change autosave timer to 2.5sec * sort categorical metadata render order so it remains consistent * add temporary autogenerated label for add-new-label operation * fix hover-over label menu interference with cell highlighting * remove debugging code * add missing reducer cases & fix typo * make dataframe memoize more general purpose * add dev mode for annos * fix error on select duplicate * handle zero occupancy categories * correctly maintain unclipped AND clipped world * correctly handle zero length FBS matrix and label files * ensure all writable categorical schema contains an unassigned category * handle case where building occupancy stack for category with no members * dialog for creating label, disable button if duplicate or empty * visually separate writeable * edit category * fix edit category name * remove debugging code * fix edit annotation label * visually define unassigned, change options * Pull in requirements.txt from `master` * label currently selected cells * duplicate label * lint * fix pytest merge issues * rename --label-file to --experimental-label-file * remove debugging console log * spelling error fix; fix bug found in PR review. * lint
This commit is contained in:
Bruce Martin
committed by
Colin Megill
Colin Megill
parent
ab2c423006
commit
3660a6cc27
@@ -0,0 +1,88 @@
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/*
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Reducers for annotation UI-state.
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*/
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const Annotations = (
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state = {
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isEditingCategoryName: false,
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isEditingLabelName: false,
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categoryEditable: false,
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labelEditable: { category: null, label: null }
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},
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action
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) => {
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switch (action.type) {
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/* CATEGORY */
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case "annotation: activate add new label mode":
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console.log(action.type, action);
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return {
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...state,
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isAddingNewLabel: true,
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categoryAddingNewLabel: action.data
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};
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case "annotation: disable add new label mode":
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return {
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...state,
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isAddingNewLabel: false,
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categoryAddingNewLabel: null
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};
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case "annotation: add new label to category":
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console.log(action.type, action);
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return {
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...state,
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isAddingNewLabel: false,
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categoryAddingNewLabel: null
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};
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case "annotation: activate category edit mode":
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console.log(action.type, action);
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return {
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...state,
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isEditingCategoryName: true,
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categoryEditable: action.data
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};
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case "annotation: disable category edit mode":
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console.log(action.type, action);
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return {
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...state,
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isEditingCategoryName: false,
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categoryEditable: null
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};
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case "annotation: category edited":
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console.log(action.type, action);
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return {
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...state,
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isEditingCategoryName: true,
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categoryEditable: null
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};
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/* LABEL */
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case "annotation: activate edit label mode":
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console.log(action.type, action);
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return {
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...state,
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isEditingLabelName: true,
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labelEditable: {
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category: action.metadataField,
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label: action.categoryIndex
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}
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};
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case "annotation: cancel edit label mode":
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console.log(action.type, action);
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return {
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...state,
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isEditingLabelName: false,
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labelEditable: { category: null, label: null }
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};
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case "annotation: label edited":
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console.log(action.type, action);
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return {
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...state,
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isEditingLabelName: false,
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labelEditable: { category: null, label: null }
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/* Bruce to persist new label name */
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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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export default Annotations;
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@@ -0,0 +1,53 @@
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const Autosave = (
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state = {
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saveInProgress: false,
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error: false,
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lastSavedObsAnnotations: null
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},
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action,
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nextSharedState
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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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/* don't save on init */
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const { universe } = nextSharedState;
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return {
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...state,
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error: false,
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saveInProgress: false,
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lastSavedObsAnnotations: universe.obsAnnotations
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};
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}
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case "writable obs annotations - save started": {
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return {
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...state,
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saveInProgress: true
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};
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}
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case "writable obs annotations - save error": {
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const { message } = action;
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return {
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...state,
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error: message,
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saveInProgress: false
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};
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}
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case "writable obs annotations - save complete": {
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const lastSavedObsAnnotations = action.obsAnnotations;
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return {
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...state,
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saveInProgress: false,
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error: false,
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lastSavedObsAnnotations
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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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export default Autosave;
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@@ -1,4 +1,4 @@
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import { ControlsHelpers } from "../util/stateManager";
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import { ControlsHelpers as CH } from "../util/stateManager";
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import * as globals from "../globals";
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function maxCategoryItems(state) {
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@@ -20,10 +20,11 @@ const CategoricalSelection = (
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case "reset World to eq Universe":
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case "set clip quantiles": {
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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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const newState = CH.createCategoricalSelection(
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world,
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CH.selectableCategoryNames(world, maxCategoryItems(prevSharedState))
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);
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return newState;
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}
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case "categorical metadata filter select": {
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@@ -96,6 +97,43 @@ const CategoricalSelection = (
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return newCategoricalSelection;
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}
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case "annotation: create category": {
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const { world } = nextSharedState;
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const name = action.data;
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return {
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...state,
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...CH.createCategoricalSelection(world, [name])
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};
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}
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case "annotation: category edited": {
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const name = action.metadataField;
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const newName = action.newCategoryText;
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const { [name]: catSeln, ...newState } = state;
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newState[newName] = catSeln;
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return newState;
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}
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case "annotation: delete category": {
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const name = action.metadataField;
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const { [name]: _, ...newState } = state;
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return newState;
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}
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case "annotation: label current cell selection":
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case "annotation: add new label to category":
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case "annotation: label edited":
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case "annotation: delete label": {
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/* need to rebuild the state for this annotation */
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const { world } = nextSharedState;
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const name = action.metadataField;
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const { [name]: _, ...partialState } = state;
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return {
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...partialState,
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...CH.createCategoricalSelection(world, [name])
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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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@@ -108,6 +108,27 @@ const ColorsReducer = (
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};
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}
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case "annotation: add new label to category":
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case "annotation: label current cell selection":
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case "annotation: delete label": {
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const { world } = nextSharedState;
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const { colorMode, colorAccessor } = state;
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const { metadataField } = action;
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if (
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colorMode !== "color by categorical metadata" ||
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colorAccessor !== metadataField
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)
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return state;
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/* else, we need to rebuild colors as labels have changed! */
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const { rgb, scale } = ColorHelpers.createColors(
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world,
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colorMode,
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colorAccessor
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);
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return { ...state, rgb, scale };
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}
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case "clear differential expression": {
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const { world: prevWorld, controls: prevControls } = prevSharedState;
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const resetColorState = ColorHelpers.checkIfColorByDiffexpAndResetColors(
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Vendored
+1
-1
@@ -7,7 +7,7 @@ import { WorldUtil } from "../util/stateManager";
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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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loading: true,
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error: null,
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// all of the data + selection state
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@@ -1,7 +1,11 @@
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import _ from "lodash";
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import Crossfilter from "../util/typedCrossfilter";
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import { World, ControlsHelpers } from "../util/stateManager";
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import {
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World,
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ControlsHelpers as CH,
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AnnotationsHelpers as AH
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} from "../util/stateManager";
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import {
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layoutDimensionName,
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obsAnnoDimensionName,
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@@ -12,7 +16,7 @@ import {
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const XYDimName = layoutDimensionName("XY");
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const CrossfilterReducer = (
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const CrossfilterReducerBase = (
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state = null,
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action,
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nextSharedState,
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@@ -32,12 +36,14 @@ const CrossfilterReducer = (
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case "reset World to eq Universe": {
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const { userDefinedGenes, diffexpGenes } = prevSharedState.controls;
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const { world } = nextSharedState;
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const crossfilter = ControlsHelpers.createGeneDimensions(
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let { crossfilter } = prevSharedState.resetCache;
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crossfilter = CH.createGeneDimensions(
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userDefinedGenes,
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diffexpGenes,
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world,
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prevSharedState.resetCache.crossfilter
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crossfilter
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);
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crossfilter = AH.createWritableAnnotationDimensions(world, crossfilter);
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return crossfilter;
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}
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@@ -51,7 +57,7 @@ const CrossfilterReducer = (
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world,
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layoutChoice.currentDimNames
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);
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crossfilter = ControlsHelpers.createGeneDimensions(
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crossfilter = CH.createGeneDimensions(
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userDefinedGenes,
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diffexpGenes,
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world,
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@@ -136,6 +142,37 @@ const CrossfilterReducer = (
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return crossfilter;
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}
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case "annotation: create category": {
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const name = action.data;
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const { world } = nextSharedState;
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const colData = world.obsAnnotations.col(name).asArray();
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return state.addDimension(obsAnnoDimensionName(name), "enum", colData);
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}
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case "annotation: category edited": {
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const name = action.metadataField;
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const newName = action.newCategoryText;
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return state.renameDimension(
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obsAnnoDimensionName(name),
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obsAnnoDimensionName(newName)
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);
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}
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case "annotation: delete category": {
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return state.delDimension(obsAnnoDimensionName(action.metadataField));
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}
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case "annotation: label current cell selection":
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case "annotation: label edited":
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case "annotation: delete label": {
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/* we need to reindex the dimension. For now, just drop it and add another */
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const name = action.metadataField;
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const dimName = obsAnnoDimensionName(name);
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const { world } = nextSharedState;
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const colData = world.obsAnnotations.col(name).asArray();
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return state.delDimension(dimName).addDimension(dimName, "enum", colData);
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}
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case "graph brush end":
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case "graph brush change": {
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const [minX, maxY] = action.brushCoords.northwest;
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@@ -185,12 +222,12 @@ const CrossfilterReducer = (
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case "categorical metadata filter select":
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case "categorical metadata filter deselect": {
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const { categoricalSelection } = nextSharedState;
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const { world } = prevSharedState;
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const cat = categoricalSelection[action.metadataField];
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const col = world.obsAnnotations.col(action.metadataField);
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const { categoryValues, categoryValueSelected } = cat;
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const values = categoryValues.filter((v, i) => categoryValueSelected[i]);
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return state.select(obsAnnoDimensionName(action.metadataField), {
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mode: "exact",
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values: ControlsHelpers.selectedValuesForCategory(cat, col)
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values
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});
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}
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@@ -212,4 +249,29 @@ const CrossfilterReducer = (
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}
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};
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/*
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IMPORTANT: the system assumes that crossfilter.data() will point at the
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same value as world.obsAnnotations. For actions handled in this reducer,
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make sure that this remains true.
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This wrapper performs only this function.
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*/
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const CrossfilterReducer = (
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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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const nextState = CrossfilterReducerBase(
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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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if (!nextState || nextState.all() === nextSharedState.world.obsAnnotations) {
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return nextState;
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}
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return nextState.setData(nextSharedState.world.obsAnnotations);
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};
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export default CrossfilterReducer;
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@@ -17,38 +17,44 @@ import responsive from "./responsive";
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import controls from "./controls";
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import resetCache from "./resetCache";
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import centroidLabel from "./centroidLabel";
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import annotations from "./annotations";
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import autosave from "./autosave";
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import undoableConfig from "./undoableConfig";
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const Reducer = undoable(
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cascadeReducers([
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["config", config],
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["universe", universe],
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["world", world],
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["layoutChoice", layoutChoice],
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["categoricalSelection", categoricalSelection],
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["continuousSelection", continuousSelection],
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["graphSelection", graphSelection],
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["crossfilter", crossfilter],
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["colors", colors],
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["controls", controls],
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["differential", differential],
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["responsive", responsive],
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["centroidLabel", centroidLabel],
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["resetCache", resetCache]
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]),
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[
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"world",
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"categoricalSelection",
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"continuousSelection",
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"graphSelection",
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"crossfilter",
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"colors",
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"controls",
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"differential",
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"layoutChoice"
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],
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undoableConfig
|
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cascadeReducers([
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["config", config],
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["universe", universe],
|
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["world", world],
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["annotations", annotations],
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["layoutChoice", layoutChoice],
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["categoricalSelection", categoricalSelection],
|
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["continuousSelection", continuousSelection],
|
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["graphSelection", graphSelection],
|
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["crossfilter", crossfilter],
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["colors", colors],
|
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["controls", controls],
|
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["differential", differential],
|
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["responsive", responsive],
|
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["centroidLabel", centroidLabel],
|
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["autosave", autosave],
|
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["resetCache", resetCache]
|
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]),
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[
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"universe",
|
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"world",
|
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"categoricalSelection",
|
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"continuousSelection",
|
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"graphSelection",
|
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"crossfilter",
|
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"colors",
|
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"controls",
|
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"differential",
|
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"layoutChoice",
|
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"annotations"
|
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],
|
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undoableConfig
|
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);
|
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|
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const store = createStore(Reducer, applyMiddleware(thunk));
|
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|
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@@ -1,13 +1,13 @@
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/*
|
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Reducer which caches derived state to be used in a reset or other
|
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recomputation.
|
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recomputation. Add stuff here you want stashed at init time (or whenever),
|
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for later use.
|
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|
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Currently this only caches the baseline (full universe) world & crossfilter,
|
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for use in a Reset.
|
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Currently this only caches the baseline (full universe) crossfilter,
|
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which improves Reset UI performance.
|
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*/
|
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const ResetCacheReducer = (
|
||||
state = {
|
||||
world: null,
|
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crossfilter: null
|
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},
|
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action,
|
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@@ -15,10 +15,9 @@ const ResetCacheReducer = (
|
||||
) => {
|
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switch (action.type) {
|
||||
case "initial data load complete (universe exists)": {
|
||||
const { world, crossfilter } = nextSharedState;
|
||||
const { crossfilter } = nextSharedState;
|
||||
return {
|
||||
...state,
|
||||
world,
|
||||
crossfilter
|
||||
};
|
||||
}
|
||||
|
||||
@@ -78,7 +78,15 @@ const saveOnActions = new Set([
|
||||
"set clip quantiles",
|
||||
|
||||
"set layout choice",
|
||||
"change graph interaction mode"
|
||||
"change graph interaction mode",
|
||||
|
||||
// user editable annotations
|
||||
"annotation: create category",
|
||||
"annotation: add new label to category",
|
||||
"annotation: delete category",
|
||||
"annotation: label edited",
|
||||
"annotation: label current cell selection",
|
||||
"annotation: delete label"
|
||||
]);
|
||||
|
||||
/**
|
||||
|
||||
@@ -1,4 +1,9 @@
|
||||
import { ControlsHelpers } from "../util/stateManager";
|
||||
import { unassignedCategoryLabel } from "../globals";
|
||||
import {
|
||||
World,
|
||||
ControlsHelpers as CH,
|
||||
AnnotationsHelpers as AH
|
||||
} from "../util/stateManager";
|
||||
|
||||
const Universe = (state = null, action, nextSharedState, prevSharedState) => {
|
||||
switch (action.type) {
|
||||
@@ -30,12 +35,186 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
|
||||
Object.keys(action.expressionData)
|
||||
)
|
||||
];
|
||||
varData = ControlsHelpers.pruneVarDataCache(varData, allTheGenesWeNeed);
|
||||
varData = CH.pruneVarDataCache(varData, allTheGenesWeNeed);
|
||||
return { ...state, varData };
|
||||
}
|
||||
|
||||
return {
|
||||
...state,
|
||||
varData
|
||||
case "annotation: create category": {
|
||||
/* create a new annotation category, with all values set to 'unassigned' */
|
||||
const name = action.data;
|
||||
const { categoryToDuplicate } = action;
|
||||
|
||||
/* name must be a string, non-zero length */
|
||||
if (typeof name !== "string" || name.length === 0)
|
||||
throw new Error("user annotations require string name");
|
||||
|
||||
/* ensure the name isn't already in use! */
|
||||
if (state.obsAnnotations.hasCol(name))
|
||||
throw new Error("name collision on annotation category create");
|
||||
|
||||
/* ensure the duplicate col exists */
|
||||
if (
|
||||
categoryToDuplicate &&
|
||||
!state.obsAnnotations.hasCol(categoryToDuplicate)
|
||||
)
|
||||
throw new Error("categoryToDuplicate does not exist");
|
||||
|
||||
let schema;
|
||||
let data;
|
||||
if (categoryToDuplicate) {
|
||||
/* duplicate the named annotation */
|
||||
schema = AH.dupObsAnnoSchema(state.schema, categoryToDuplicate, name, {
|
||||
writable: true
|
||||
});
|
||||
/* if we are duplicating a non-writable annotation, it may not have an unassigned category */
|
||||
const s = schema.annotations.obsByName[categoryToDuplicate];
|
||||
if (s.categories.indexOf(unassignedCategoryLabel) === -1) {
|
||||
s.categories = s.categories.concat(unassignedCategoryLabel);
|
||||
}
|
||||
data = state.obsAnnotations.col(categoryToDuplicate).asArray();
|
||||
} else {
|
||||
/* else, all are unassined */
|
||||
const categories = [unassignedCategoryLabel];
|
||||
schema = AH.addObsAnnoSchema(state.schema, name, {
|
||||
name,
|
||||
categories,
|
||||
type: "categorical",
|
||||
writable: true
|
||||
});
|
||||
data = new Array(state.nObs).fill(unassignedCategoryLabel);
|
||||
}
|
||||
|
||||
const obsAnnotations = state.obsAnnotations.withCol(name, data);
|
||||
return { ...state, obsAnnotations, schema };
|
||||
}
|
||||
|
||||
case "annotation: category edited": {
|
||||
/* change the name of an obs annotation category */
|
||||
const name = action.metadataField;
|
||||
const newName = action.newCategoryText;
|
||||
if (!AH.isUserAnnotation(state, name))
|
||||
throw new Error("unable to edit read-only annotation");
|
||||
if (typeof newName !== "string" || newName.length === 0)
|
||||
throw new Error("user annotations require string name");
|
||||
|
||||
const colSchema = {
|
||||
...state.schema.annotations.obsByName[name],
|
||||
name: newName
|
||||
};
|
||||
const schema = AH.addObsAnnoSchema(
|
||||
AH.removeObsAnnoSchema(state.schema, name),
|
||||
newName,
|
||||
colSchema
|
||||
);
|
||||
const obsAnnotations = state.obsAnnotations.renameCol(name, newName);
|
||||
return { ...state, schema, obsAnnotations };
|
||||
}
|
||||
|
||||
case "annotation: delete category": {
|
||||
/* delete annotation category from schema and obsAnnotations */
|
||||
const name = action.metadataField;
|
||||
if (!AH.isUserAnnotation(state, name))
|
||||
throw new Error("unable to delete read-only annotation");
|
||||
|
||||
const schema = AH.removeObsAnnoSchema(state.schema, name);
|
||||
const obsAnnotations = state.obsAnnotations.dropCol(name);
|
||||
return { ...state, schema, obsAnnotations };
|
||||
}
|
||||
|
||||
case "annotation: add new label to category": {
|
||||
const annotationName = action.metadataField;
|
||||
const newLabelName = action.newLabelText;
|
||||
if (!AH.isUserAnnotation(state, annotationName))
|
||||
throw new Error("unable to modify read-only annotation");
|
||||
if (typeof newLabelName !== "string" || newLabelName.length === 0)
|
||||
throw new Error(
|
||||
"user annotations require a non-zero length string name"
|
||||
);
|
||||
|
||||
/* add the new label to the annotation */
|
||||
const schema = AH.addObsAnnoCategory(
|
||||
state.schema,
|
||||
annotationName,
|
||||
newLabelName
|
||||
);
|
||||
return { ...state, schema };
|
||||
}
|
||||
|
||||
case "annotation: label edited": {
|
||||
const annotationName = action.metadataField;
|
||||
const oldLabelName = action.label;
|
||||
const newLabelName = action.editedLabel;
|
||||
if (!AH.isUserAnnotation(state, annotationName))
|
||||
throw new Error("unable to modify read-only annotation");
|
||||
if (typeof newLabelName !== "string" || newLabelName.length === 0)
|
||||
throw new Error(
|
||||
"user annotations require a non-zero length string name"
|
||||
);
|
||||
|
||||
/* remove old label, add new label */
|
||||
const schema = AH.addObsAnnoCategory(
|
||||
AH.removeObsAnnoCategory(state.schema, annotationName, oldLabelName),
|
||||
annotationName,
|
||||
newLabelName
|
||||
);
|
||||
|
||||
/* change all values in obsAnnotation */
|
||||
const obsAnnotations = AH.setLabelByValue(
|
||||
state.obsAnnotations,
|
||||
annotationName,
|
||||
oldLabelName,
|
||||
newLabelName
|
||||
);
|
||||
|
||||
return { ...state, schema, obsAnnotations };
|
||||
}
|
||||
|
||||
case "annotation: delete label": {
|
||||
/* delete the label from the annotation, and set all cells with this value to unassigned */
|
||||
const annotationName = action.metadataField;
|
||||
const labelName = action.label;
|
||||
if (!AH.isUserAnnotation(state, annotationName))
|
||||
throw new Error("unable to modify read-only annotation");
|
||||
if (labelName === unassignedCategoryLabel)
|
||||
throw new Error("may not remove the unassigned label");
|
||||
|
||||
/* remove the category from the schema */
|
||||
const schema = AH.removeObsAnnoCategory(
|
||||
state.schema,
|
||||
annotationName,
|
||||
labelName
|
||||
);
|
||||
|
||||
/* set all values to unassigned in obsAnnotations */
|
||||
const obsAnnotations = AH.setLabelByValue(
|
||||
state.obsAnnotations,
|
||||
annotationName,
|
||||
labelName,
|
||||
unassignedCategoryLabel
|
||||
);
|
||||
|
||||
return { ...state, schema, obsAnnotations };
|
||||
}
|
||||
|
||||
case "annotation: label current cell selection": {
|
||||
const { metadataField, label } = action;
|
||||
const { world, crossfilter } = prevSharedState;
|
||||
|
||||
/*
|
||||
selection state is relative to world. We need to convert it
|
||||
to a mask for Universe before applying it.
|
||||
*/
|
||||
const worldMask = crossfilter.allSelectedMask();
|
||||
const mask = World.worldEqUniverse(world, state)
|
||||
? worldMask
|
||||
: AH.worldToUniverseMask(worldMask, world.obsAnnotations, state.nObs);
|
||||
const obsAnnotations = AH.setLabelByMask(
|
||||
state.obsAnnotations,
|
||||
metadataField,
|
||||
mask,
|
||||
label
|
||||
);
|
||||
return { ...state, obsAnnotations };
|
||||
}
|
||||
|
||||
default: {
|
||||
|
||||
@@ -1,7 +1,22 @@
|
||||
import { World, ControlsHelpers } from "../util/stateManager";
|
||||
import { unassignedCategoryLabel } from "../globals";
|
||||
import {
|
||||
World,
|
||||
ControlsHelpers as CH,
|
||||
AnnotationsHelpers as AH
|
||||
} from "../util/stateManager";
|
||||
import clip from "../util/clip";
|
||||
import quantile from "../util/quantile";
|
||||
|
||||
/*
|
||||
important note: much of this code assumes that wriable (user) annotations
|
||||
will NOT contain scalar data (ie, will only contain categorical labelled
|
||||
data), and therefore will never need to be clipped. Put another way, it
|
||||
assumes that for these annotations, the clipped & unclipped data is equal.
|
||||
|
||||
If we ever start allowing user editable scalar data, this assumption will
|
||||
need to be revisited.
|
||||
*/
|
||||
|
||||
const WorldReducer = (
|
||||
state = null,
|
||||
action,
|
||||
@@ -9,16 +24,13 @@ const WorldReducer = (
|
||||
prevSharedState
|
||||
) => {
|
||||
switch (action.type) {
|
||||
case "initial data load complete (universe exists)": {
|
||||
case "initial data load complete (universe exists)":
|
||||
case "reset World to eq Universe": {
|
||||
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.createWorldBySelection(
|
||||
@@ -80,7 +92,7 @@ const WorldReducer = (
|
||||
Object.keys(action.expressionData)
|
||||
)
|
||||
];
|
||||
unclippedVarData = ControlsHelpers.pruneVarDataCache(
|
||||
unclippedVarData = CH.pruneVarDataCache(
|
||||
unclippedVarData,
|
||||
allTheGenesWeNeed
|
||||
);
|
||||
@@ -122,6 +134,135 @@ const WorldReducer = (
|
||||
};
|
||||
}
|
||||
|
||||
case "annotation: create category": {
|
||||
const name = action.data;
|
||||
const { universe } = nextSharedState;
|
||||
const { schema } = universe;
|
||||
|
||||
/*
|
||||
if world !== universe, we have to subset the newly created annotation,
|
||||
else, just use it as is.
|
||||
*/
|
||||
let newAnnotation = null;
|
||||
if (!World.worldEqUniverse(state, universe)) {
|
||||
newAnnotation = universe.obsAnnotations
|
||||
.subset(state.obsAnnotations.rowIndex.keys(), [name], null)
|
||||
.icol(0)
|
||||
.asArray();
|
||||
} else {
|
||||
newAnnotation = universe.obsAnnotations.col(name).asArray();
|
||||
}
|
||||
const obsAnnotations = state.obsAnnotations.withCol(
|
||||
name,
|
||||
newAnnotation,
|
||||
state.obsAnnotations.rowIndex
|
||||
);
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: state.unclipped.obsAnnotations.withCol(
|
||||
name,
|
||||
newAnnotation,
|
||||
state.unclipped.obsAnnotations.rowIndex
|
||||
)
|
||||
};
|
||||
return { ...state, schema, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
case "annotation: category edited": {
|
||||
/* change the name of an obs annotation */
|
||||
const name = action.metadataField;
|
||||
const newName = action.newCategoryText;
|
||||
const { schema } = nextSharedState.universe;
|
||||
const obsAnnotations = state.obsAnnotations.renameCol(name, newName);
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: state.unclipped.obsAnnotations.renameCol(name, newName)
|
||||
};
|
||||
return { ...state, schema, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
case "annotation: delete category": {
|
||||
/* remove a category from obs annotation */
|
||||
const { schema } = nextSharedState.universe;
|
||||
const name = action.metadataField;
|
||||
const obsAnnotations = state.obsAnnotations.dropCol(name);
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: state.unclipped.obsAnnotations.dropCol(name)
|
||||
};
|
||||
return { ...state, schema, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
case "annotation: add new label to category": {
|
||||
/* add a new label to the schema - schema updated by universe reducer, we just need to note it */
|
||||
const { schema } = nextSharedState.universe;
|
||||
return { ...state, schema };
|
||||
}
|
||||
|
||||
case "annotation: label edited": {
|
||||
const { schema } = nextSharedState.universe;
|
||||
const { metadataField } = action;
|
||||
const oldLabelName = action.label;
|
||||
const newLabelName = action.editedLabel;
|
||||
|
||||
/* set all values to to new label */
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: AH.setLabelByValue(
|
||||
state.unclipped.obsAnnotations,
|
||||
metadataField,
|
||||
oldLabelName,
|
||||
newLabelName
|
||||
)
|
||||
};
|
||||
const obsAnnotations = state.obsAnnotations.replaceColData(
|
||||
metadataField,
|
||||
unclipped.obsAnnotations.col(metadataField).asArray()
|
||||
);
|
||||
return { ...state, schema, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
case "annotation: delete label": {
|
||||
const { schema } = nextSharedState.universe;
|
||||
const { label, metadataField } = action;
|
||||
|
||||
/* set all values to unassigned in obsAnnotations */
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: AH.setLabelByValue(
|
||||
state.unclipped.obsAnnotations,
|
||||
metadataField,
|
||||
label,
|
||||
unassignedCategoryLabel
|
||||
)
|
||||
};
|
||||
const obsAnnotations = state.obsAnnotations.replaceColData(
|
||||
metadataField,
|
||||
unclipped.obsAnnotations.col(metadataField).asArray()
|
||||
);
|
||||
return { ...state, schema, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
case "annotation: label current cell selection": {
|
||||
const { metadataField, label } = action;
|
||||
const { crossfilter } = prevSharedState;
|
||||
const mask = crossfilter.allSelectedMask();
|
||||
const unclipped = {
|
||||
...state.unclipped,
|
||||
obsAnnotations: AH.setLabelByMask(
|
||||
state.unclipped.obsAnnotations,
|
||||
metadataField,
|
||||
mask,
|
||||
label
|
||||
)
|
||||
};
|
||||
const obsAnnotations = state.obsAnnotations.replaceColData(
|
||||
metadataField,
|
||||
unclipped.obsAnnotations.col(metadataField).asArray()
|
||||
);
|
||||
return { ...state, obsAnnotations, unclipped };
|
||||
}
|
||||
|
||||
default: {
|
||||
return state;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user