mirror of
https://github.com/chanzuckerberg/cellxgene.git
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Handle loading state when rendering categories with one label (#1393)
* refactor & loading state * truncate * fix minor PR review issues * lint Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
This commit is contained in:
Colin Megill
co-authored by
bkmartinjr
bkmartinjr
parent
7d4d360e52
commit
ea434fc46f
@@ -0,0 +1,587 @@
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import { connect } from "react-redux";
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import React from "react";
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import {
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Button,
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Menu,
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MenuItem,
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Popover,
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Position,
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PopoverInteractionKind,
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Tooltip,
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} from "@blueprintjs/core";
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import Occupancy from "./occupancy";
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import * as globals from "../../../globals";
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import styles from "../categorical.css";
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import AnnoDialog from "../annoDialog";
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import LabelInput from "../labelInput";
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import { AnnotationsHelpers } from "../../../util/stateManager";
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import { labelPrompt, isLabelErroneous } from "../labelUtil";
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/* this is defined outside of the class so we can use it in connect() */
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function _currentLabel(ownProps, categoricalSelection) {
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const { metadataField, categoryIndex } = ownProps;
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return String(
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categoricalSelection[metadataField].categoryValues[categoryIndex]
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).valueOf();
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}
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@connect((state, ownProps) => {
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const { pointDilation, categoricalSelection } = state;
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const { metadataField } = ownProps;
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const isDilated =
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pointDilation.metadataField === metadataField &&
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pointDilation.categoryField ===
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_currentLabel(ownProps, categoricalSelection);
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return {
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categoricalSelection,
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annotations: state.annotations,
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colorScale: state.colors.scale,
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colorAccessor: state.colors.colorAccessor,
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schema: state.world?.schema,
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world: state.world,
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crossfilter: state.crossfilter,
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ontology: state.ontology,
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isDilated,
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};
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})
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class CategoryValue extends React.Component {
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constructor(props) {
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super(props);
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this.state = {
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editedLabelText: this.currentLabel(),
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};
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}
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componentDidUpdate(prevProps) {
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const { categoricalSelection, metadataField, categoryIndex } = this.props;
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if (
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prevProps.categoricalSelection !== categoricalSelection ||
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prevProps.metadataField !== metadataField ||
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prevProps.categoryIndex !== categoryIndex
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) {
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this.setState({
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editedLabelText: this.currentLabel(),
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});
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}
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}
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handleDeleteValue = () => {
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const { dispatch, metadataField } = this.props;
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const label = this.getLabel();
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dispatch({
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type: "annotation: delete label",
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metadataField,
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label,
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});
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};
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handleAddCurrentSelectionToThisLabel = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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const label = this.getLabel();
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dispatch({
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type: "annotation: label current cell selection",
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metadataField,
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categoryIndex,
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label,
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});
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};
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handleEditValue = (e) => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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const { editedLabelText } = this.state;
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const label = this.getLabel();
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this.cancelEditMode();
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dispatch({
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type: "annotation: label edited",
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editedLabel: editedLabelText,
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metadataField,
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categoryIndex,
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label,
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});
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e.preventDefault();
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};
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handleCreateArbitraryLabel = (txt) => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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const label = this.getLabel();
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this.cancelEditMode();
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dispatch({
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type: "annotation: label edited",
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metadataField,
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editedLabel: txt,
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categoryIndex,
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label,
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});
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};
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labelNameError = (name) => {
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const { metadataField, ontology, schema } = this.props;
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if (name === this.currentLabel()) return false;
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return isLabelErroneous(name, metadataField, ontology, schema);
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};
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instruction = (label) => {
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return labelPrompt(this.labelNameError(label), "New, unique label", ":");
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};
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activateEditLabelMode = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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dispatch({
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type: "annotation: activate edit label mode",
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metadataField,
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categoryIndex,
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});
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};
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cancelEditMode = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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this.setState({
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editedLabelText: this.currentLabel(),
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});
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dispatch({
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type: "annotation: cancel edit label mode",
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metadataField,
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categoryIndex,
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});
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};
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toggleOff = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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dispatch({
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type: "categorical metadata filter deselect",
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metadataField,
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categoryIndex,
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});
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};
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shouldComponentUpdate = (nextProps, nextState) => {
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/*
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Checks to see if at least one of the following changed:
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* world state
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* the color accessor (what is currently being colored by)
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* if this catagorical value's selection status has changed
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* the crossfilter (ie, global selection state)
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If and only if true, update the component
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*/
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const { props, state } = this;
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const { metadataField, categoryIndex, categoricalSelection } = props;
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const { categoricalSelection: newCategoricalSelection } = nextProps;
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const valueSelectionChange =
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categoricalSelection[metadataField].categoryValueSelected[
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categoryIndex
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] !==
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newCategoricalSelection[metadataField].categoryValueSelected[
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categoryIndex
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];
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const worldChange = props.world !== nextProps.world;
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const colorAccessorChange = props.colorAccessor !== nextProps.colorAccessor;
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const annotationsChange = props.annotations !== nextProps.annotations;
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const crossfilterChange =
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props.isUserAnno && props.crossfilter !== nextProps.crossfilter;
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const editingLabel = state.editedLabelText !== nextState.editedLabelText;
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const dilationChange = props.isDilated !== nextProps.isDilated;
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return (
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valueSelectionChange ||
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worldChange ||
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colorAccessorChange ||
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annotationsChange ||
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crossfilterChange ||
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editingLabel ||
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dilationChange
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);
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};
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toggleOn = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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dispatch({
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type: "categorical metadata filter select",
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metadataField,
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categoryIndex,
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});
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};
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handleMouseEnter = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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dispatch({
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type: "category value mouse hover start",
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metadataField,
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categoryIndex,
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});
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};
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handleMouseExit = () => {
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const { dispatch, metadataField, categoryIndex } = this.props;
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dispatch({
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type: "category value mouse hover end",
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metadataField,
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categoryIndex,
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});
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};
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handleTextChange = (text) => {
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this.setState({ editedLabelText: text });
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};
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handleChoice = (e) => {
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/* Blueprint Suggest format */
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this.setState({ editedLabelText: e.target });
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};
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getLabel = () => {
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const { metadataField, categoryIndex, categoricalSelection } = this.props;
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const category = categoricalSelection[metadataField];
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const label = category.categoryValues[categoryIndex];
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return label;
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};
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currentLabel() {
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const { categoricalSelection } = this.props;
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return _currentLabel(this.props, categoricalSelection);
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}
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isAddCurrentSelectionDisabled(category, value) {
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/*
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disable "add current selection to label", if one of the following is true:
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1. no cells are selected
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2. all currently selected cells already have this label, on this category
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*/
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const { crossfilter, world } = this.props;
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// 1. no cells selected?
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if (crossfilter.countSelected() === 0) {
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return true;
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}
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// 2. all selected cells already have the label
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const mask = crossfilter.allSelectedMask();
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if (
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AnnotationsHelpers.allHaveLabelByMask(
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world.obsAnnotations,
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category,
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value,
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mask
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)
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) {
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return true;
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}
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// else, don't disable
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return false;
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}
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render() {
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const {
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categoricalSelection,
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metadataField,
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categoryIndex,
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colorAccessor,
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colorScale,
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i,
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schema,
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isUserAnno,
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annotations,
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ontology,
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// flippedProps is potentially brittle, their docs want {...flippedProps} on our div,
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// our lint doesn't like jsx spread, we are version pinned to prevent api change on their part
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flippedProps,
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isDilated,
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} = this.props;
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const ontologyEnabled = ontology?.enabled ?? false;
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const { editedLabelText } = this.state;
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if (!categoricalSelection) return null;
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const category = categoricalSelection[metadataField];
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const selected = category.categoryValueSelected[categoryIndex];
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const count = category.categoryValueCounts[categoryIndex];
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const value = category.categoryValues[categoryIndex];
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const displayString = this.currentLabel();
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/* this is the color scale, so add swatches below */
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const isColorBy = metadataField === colorAccessor;
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let categories = null;
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if (isColorBy && schema) {
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categories = schema.annotations.obsByName[colorAccessor]?.categories;
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}
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let truncatedString = null;
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if (
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colorAccessor &&
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!isColorBy &&
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displayString.length > globals.categoryLabelDisplayStringShortLength
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) {
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truncatedString = `${displayString.slice(
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0,
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globals.categoryLabelDisplayStringShortLength / 2
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)}…${displayString.slice(
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-globals.categoryLabelDisplayStringShortLength / 2
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)}`;
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} else if (
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displayString.length > globals.categoryLabelDisplayStringLongLength
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) {
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truncatedString = `${displayString.slice(
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0,
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globals.categoryLabelDisplayStringLongLength / 2
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)}…${displayString.slice(
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-globals.categoryLabelDisplayStringLongLength / 2
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)}`;
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}
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const editModeActive =
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isUserAnno &&
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annotations.labelEditable.category === metadataField &&
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annotations.isEditingLabelName &&
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annotations.labelEditable.label === categoryIndex;
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return (
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<div
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key={i}
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data-flip-config={flippedProps["data-flip-config"]}
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data-flip-id={flippedProps["data-flip-id"]}
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data-portal-key={flippedProps["data-portal-key"]}
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className={
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/* This code is to change the styles on centroid label hover is causing over-rendering */
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`${styles.value}${isDilated ? ` ${styles.hover}` : ""}`
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}
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data-testclass="categorical-row"
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style={{
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padding: "4px 7px",
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display: "flex",
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alignItems: "baseline",
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justifyContent: "space-between",
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marginBottom: "2px",
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borderRadius: "2px",
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}}
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onMouseEnter={this.handleMouseEnter}
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onMouseLeave={this.handleMouseExit}
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>
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<div
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style={{
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margin: 0,
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padding: 0,
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userSelect: "none",
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width: globals.leftSidebarWidth - 145,
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display: "flex",
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justifyContent: "space-between",
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}}
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>
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<div style={{ display: "flex", alignItems: "baseline" }}>
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<label className="bp3-control bp3-checkbox" style={{ margin: 0 }}>
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<input
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onChange={selected ? this.toggleOff : this.toggleOn}
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data-testclass="categorical-value-select"
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data-testid={`categorical-value-select-${metadataField}-${displayString}`}
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checked={selected}
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type="checkbox"
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/>
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<span
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className="bp3-control-indicator"
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onMouseEnter={this.handleMouseExit}
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onMouseLeave={this.handleMouseEnter}
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/>
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</label>
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<Tooltip
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content={displayString}
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disabled={truncatedString === null}
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hoverOpenDelay={globals.tooltipHoverOpenDelayQuick}
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position={Position.LEFT}
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usePortal
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modifiers={{
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preventOverflow: { enabled: false },
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hide: { enabled: false },
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}}
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>
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<span
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data-testid={`categorical-value-${metadataField}-${displayString}`}
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data-testclass="categorical-value"
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style={{
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color:
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displayString === globals.unassignedCategoryLabel
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? "#ababab"
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: "black",
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fontStyle:
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displayString === globals.unassignedCategoryLabel
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? "italic"
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: "normal",
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display: "inline-block",
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overflow: "hidden",
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lineHeight: "1.1em",
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height: "1.1em",
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wordBreak: "break-all",
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verticalAlign: "middle",
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}}
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>
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{truncatedString || displayString}
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</span>
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</Tooltip>
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{editModeActive ? (
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<div>
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<AnnoDialog
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isActive={editModeActive}
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inputProps={{
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"data-testid": `${metadataField}:edit-label-name-dialog`,
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}}
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primaryButtonProps={{
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"data-testid": `${metadataField}:${displayString}:submit-label-edit`,
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}}
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title="Edit label"
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instruction={this.instruction(editedLabelText)}
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cancelTooltipContent="Close this dialog without editing label text."
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primaryButtonText="Change label text"
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text={editedLabelText}
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categoryToDuplicate={null}
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validationError={this.labelNameError(editedLabelText)}
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handleSubmit={this.handleEditValue}
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handleCancel={this.cancelEditMode}
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annoInput={
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<LabelInput
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label={editedLabelText}
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labelSuggestions={ontologyEnabled ? ontology.terms : null}
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onChange={this.handleTextChange}
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onSelect={this.handleTextChange}
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inputProps={{
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"data-testid": `${metadataField}:${displayString}:edit-label-name`,
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leftIcon: "tag",
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intent: "none",
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autoFocus: true,
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}}
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/>
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}
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annoSelect={null}
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/>
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</div>
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) : null}
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</div>
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<span style={{ flexShrink: 0 }}>
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{colorAccessor && !isColorBy && !annotations.isEditingLabelName ? (
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<Occupancy
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category={category}
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{...this.props} // eslint-disable-line react/jsx-props-no-spreading
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/>
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) : null}
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</span>
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</div>
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<div>
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<span>
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<span
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data-testclass="categorical-value-count"
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data-testid={`categorical-value-count-${metadataField}-${displayString}`}
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style={{
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color:
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displayString === globals.unassignedCategoryLabel
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? "#ababab"
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: "black",
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fontStyle:
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displayString === globals.unassignedCategoryLabel
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? "italic"
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: "auto",
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}}
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>
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{count}
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</span>
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<svg
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display={isColorBy && categories ? "auto" : "none"}
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style={{
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marginLeft: 5,
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width: 11,
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height: 11,
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backgroundColor:
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isColorBy && categories
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? colorScale(categories.indexOf(value))
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: "inherit",
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}}
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/>
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{isUserAnno ? (
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<span
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onMouseEnter={this.handleMouseExit}
|
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onMouseLeave={this.handleMouseEnter}
|
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>
|
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<Popover
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interactionKind={PopoverInteractionKind.HOVER}
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boundary="window"
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position={Position.RIGHT_TOP}
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content={
|
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<Menu>
|
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<MenuItem
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icon="plus"
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data-testclass="handleAddCurrentSelectionToThisLabel"
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data-testid={`${metadataField}:${displayString}:add-current-selection-to-this-label`}
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onClick={this.handleAddCurrentSelectionToThisLabel}
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text={
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<span>
|
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Re-label currently selected cells as
|
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<span
|
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style={{
|
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fontStyle:
|
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displayString ===
|
||||
globals.unassignedCategoryLabel
|
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? "italic"
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: "auto",
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}}
|
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>
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{` ${displayString}`}
|
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</span>
|
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</span>
|
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}
|
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disabled={this.isAddCurrentSelectionDisabled(
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metadataField,
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value
|
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)}
|
||||
/>
|
||||
{displayString !== globals.unassignedCategoryLabel ? (
|
||||
<MenuItem
|
||||
icon="edit"
|
||||
text="Edit this label's name"
|
||||
data-testclass="handleEditValue"
|
||||
data-testid={`${metadataField}:${displayString}:edit-label`}
|
||||
onClick={this.activateEditLabelMode}
|
||||
disabled={annotations.isEditingLabelName}
|
||||
/>
|
||||
) : null}
|
||||
{displayString !== globals.unassignedCategoryLabel ? (
|
||||
<MenuItem
|
||||
icon="delete"
|
||||
intent="danger"
|
||||
data-testclass="handleDeleteValue"
|
||||
data-testid={`${metadataField}:${displayString}:delete-label`}
|
||||
onClick={this.handleDeleteValue}
|
||||
text={`Delete this label, and reassign all cells to type '${globals.unassignedCategoryLabel}'`}
|
||||
/>
|
||||
) : null}
|
||||
</Menu>
|
||||
}
|
||||
>
|
||||
<Button
|
||||
style={{
|
||||
marginLeft: 0,
|
||||
position: "relative",
|
||||
top: -1,
|
||||
minHeight: 16,
|
||||
}}
|
||||
data-testclass="seeActions"
|
||||
data-testid={`${metadataField}:${displayString}:see-actions`}
|
||||
icon="more"
|
||||
small
|
||||
minimal
|
||||
/>
|
||||
</Popover>
|
||||
</span>
|
||||
) : null}
|
||||
</span>
|
||||
</div>
|
||||
</div>
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
export default CategoryValue;
|
||||
@@ -0,0 +1,203 @@
|
||||
// jshint esversion: 6
|
||||
import React from "react";
|
||||
import { connect } from "react-redux";
|
||||
import * as d3 from "d3";
|
||||
import {
|
||||
Popover,
|
||||
PopoverInteractionKind,
|
||||
Position,
|
||||
Classes
|
||||
} from "@blueprintjs/core";
|
||||
|
||||
@connect()
|
||||
class Occupancy extends React.PureComponent {
|
||||
_WIDTH = 100;
|
||||
|
||||
_HEIGHT = 11;
|
||||
|
||||
createHistogram = () => {
|
||||
/*
|
||||
Knowing that colorScale is based off continous data,
|
||||
createHistogram fetches the continous data in relation to the cells releveant to the catagory value.
|
||||
It then seperates that data into 50 bins for drawing the mini-histogram
|
||||
*/
|
||||
const {
|
||||
world,
|
||||
metadataField,
|
||||
colorAccessor,
|
||||
category,
|
||||
categoryIndex
|
||||
} = this.props;
|
||||
|
||||
if (!this.canvas) return;
|
||||
|
||||
const groupBy = world.obsAnnotations.col(metadataField);
|
||||
|
||||
const col =
|
||||
world.obsAnnotations.col(colorAccessor) ||
|
||||
world.varData.col(colorAccessor);
|
||||
|
||||
const range = col.summarize();
|
||||
|
||||
const histogramMap = col.histogram(
|
||||
50,
|
||||
[range.min, range.max],
|
||||
groupBy
|
||||
); /* Because the signature changes we really need different names for histogram to differentiate signatures */
|
||||
|
||||
const categoryValue = category.categoryValues[categoryIndex];
|
||||
const bins = histogramMap.has(categoryValue)
|
||||
? histogramMap.get(categoryValue)
|
||||
: new Array(50).fill(0);
|
||||
|
||||
const xScale = d3
|
||||
.scaleLinear()
|
||||
.domain([0, bins.length])
|
||||
.range([0, this._WIDTH]);
|
||||
|
||||
const largestBin = Math.max(...bins);
|
||||
|
||||
const yScale = d3
|
||||
.scaleLinear()
|
||||
.domain([0, largestBin])
|
||||
.range([0, this._HEIGHT]);
|
||||
|
||||
const ctx = this.canvas.getContext("2d");
|
||||
|
||||
ctx.fillStyle = "#000";
|
||||
|
||||
let x;
|
||||
let y;
|
||||
|
||||
const rectWidth = this._WIDTH / bins.length;
|
||||
|
||||
for (let i = 0, { length } = bins; i < length; i += 1) {
|
||||
x = xScale(i);
|
||||
y = yScale(bins[i]);
|
||||
ctx.fillRect(x, this._HEIGHT - y, rectWidth, y);
|
||||
}
|
||||
};
|
||||
|
||||
createOccupancyStack = () => {
|
||||
/*
|
||||
Knowing that the color scale is based off of catagorical data,
|
||||
createOccupancyStack obtains a map showing the number if cells per colored value
|
||||
Using the colorScale a stack of colored bars is drawn representing the map
|
||||
*/
|
||||
const {
|
||||
world,
|
||||
metadataField,
|
||||
colorAccessor,
|
||||
category,
|
||||
categoryIndex,
|
||||
schema,
|
||||
colorScale
|
||||
} = this.props;
|
||||
|
||||
const ctx = this.canvas?.getContext("2d");
|
||||
|
||||
if (!ctx) return;
|
||||
|
||||
const groupBy = world.obsAnnotations.col(metadataField);
|
||||
const occupancyMap = world.obsAnnotations
|
||||
.col(colorAccessor)
|
||||
.histogramCategorical(groupBy);
|
||||
|
||||
const occupancy = occupancyMap.get(category.categoryValues[categoryIndex]);
|
||||
|
||||
if (occupancy && occupancy.size > 0) {
|
||||
// not all categories have occupancy, so occupancy may be undefined.
|
||||
const x = d3
|
||||
.scaleLinear()
|
||||
/* get all the keys d[1] as an array, then find the sum */
|
||||
.domain([0, d3.sum(Array.from(occupancy.values()))])
|
||||
.range([0, this._WIDTH]);
|
||||
const categories =
|
||||
schema.annotations.obsByName[colorAccessor]?.categories;
|
||||
|
||||
let currentOffset = 0;
|
||||
const dfColumn = world.obsAnnotations.col(colorAccessor);
|
||||
const categoryValues = dfColumn.summarizeCategorical().categories;
|
||||
|
||||
let o;
|
||||
let scaledValue;
|
||||
let value;
|
||||
|
||||
for (let i = 0, { length } = categoryValues; i < length; i += 1) {
|
||||
value = categoryValues[i];
|
||||
o = occupancy.get(value);
|
||||
scaledValue = x(o);
|
||||
ctx.fillStyle = o
|
||||
? colorScale(categories.indexOf(value))
|
||||
: "rgb(255,255,255)";
|
||||
ctx.fillRect(currentOffset, 0, o ? scaledValue : 0, this._HEIGHT);
|
||||
currentOffset += o ? scaledValue : 0;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
render() {
|
||||
const {
|
||||
colorAccessor,
|
||||
categoricalSelection,
|
||||
category,
|
||||
categoryIndex
|
||||
} = this.props;
|
||||
|
||||
const { canvas } = this;
|
||||
if (canvas)
|
||||
canvas.getContext("2d").clearRect(0, 0, this._WIDTH, this._HEIGHT);
|
||||
|
||||
const colorByIsCatagoricalData = !!categoricalSelection[colorAccessor];
|
||||
|
||||
return (
|
||||
<Popover
|
||||
interactionKind={PopoverInteractionKind.HOVER_TARGET_ONLY}
|
||||
hoverOpenDelay={1500}
|
||||
hoverCloseDelay={200}
|
||||
position={Position.LEFT}
|
||||
modifiers={{
|
||||
preventOverflow: { enabled: false },
|
||||
hide: { enabled: false }
|
||||
}}
|
||||
lazy
|
||||
usePortal
|
||||
disabled={colorByIsCatagoricalData}
|
||||
popoverClassName={Classes.POPOVER_CONTENT_SIZING}
|
||||
>
|
||||
<canvas
|
||||
className="bp3-popover-targer"
|
||||
style={{
|
||||
marginRight: 5,
|
||||
width: this._WIDTH,
|
||||
height: this._HEIGHT,
|
||||
borderBottom: colorByIsCatagoricalData
|
||||
? ""
|
||||
: "solid rgb(230, 230, 230) 0.25px"
|
||||
}}
|
||||
width={this._WIDTH}
|
||||
height={this._HEIGHT}
|
||||
ref={ref => {
|
||||
this.canvas = ref;
|
||||
if (colorByIsCatagoricalData) this.createOccupancyStack();
|
||||
else this.createHistogram();
|
||||
}}
|
||||
/>
|
||||
<div key="text" style={{ fontFamily: "Roboto", fontSize: "14px" }}>
|
||||
<p style={{ margin: "0" }}>
|
||||
This histograms shows the distribution of{" "}
|
||||
<strong>{colorAccessor}</strong> within{" "}
|
||||
<strong>{category.categoryValues[categoryIndex]}</strong>.
|
||||
<br />
|
||||
<br />
|
||||
The x axis is the same for each histogram, while the y axis is
|
||||
scaled to the largest bin within this histogram instead of the
|
||||
largest bin within the whole category.
|
||||
</p>
|
||||
</div>
|
||||
</Popover>
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
export default Occupancy;
|
||||
Reference in New Issue
Block a user