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Merge branch 'main' into colinmegill/geneset-prototype

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This commit is contained in:
Colin Megill
2020-08-17 10:49:57 -04:00
parent adb0b65058 508889f74b
commit bef631396c
271 changed files with 4546 additions and 1766 deletions
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client/src/actions/annotation.js
+19 -10
View File
@@ -34,7 +34,8 @@ export const annotationCreateCategoryAction = (
throw new Error("name collision on annotation category create");
let initialValue;
let categories;
let newSchema;
let ctor;
if (categoryToDuplicate) {
/* if we are duplicating a category, retrieve it */
const catDupSchema = schema.annotations.obsByName[categoryToDuplicate];
@@ -47,25 +48,33 @@ export const annotationCreateCategoryAction = (
.fetch("obs", categoryToDuplicate);
const col = catToDupDf.col(categoryToDuplicate);
initialValue = col.asArray();
({ categories } = col.summarize());
const { categories } = col.summarizeCategorical();
// all user-created annotations must have the unassigned category
if (!categories.includes(globals.unassignedCategoryLabel)) {
categories.push(globals.unassignedCategoryLabel);
}
ctor = initialValue.constructor;
newSchema = {
...catDupSchema,
name: newCategoryName,
categories,
writable: true,
};
} else {
/* else assign to the standard default value */
initialValue = globals.unassignedCategoryLabel;
categories = [globals.unassignedCategoryLabel];
ctor = Array;
newSchema = {
name: newCategoryName,
type: "categorical",
categories: [globals.unassignedCategoryLabel],
writable: true,
};
}
const obsCrossfilter = prevObsCrossfilter.addObsColumn(
{
name: newCategoryName,
type: "categorical",
categories,
writable: true,
},
Array,
newSchema,
ctor,
initialValue
);
client/src/actions/embedding.js
+44
View File
@@ -0,0 +1,44 @@
/*
action creators related to embeddings choice
*/
import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers";
export async function _switchEmbedding(prevAnnoMatrix, newEmbeddingName) {
/*
DRY helper used by this and reembedding action creators
*/
const base = prevAnnoMatrix.base();
const embeddingDf = await base.fetch("emb", newEmbeddingName);
const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf);
const obsCrossfilter = await new AnnoMatrixObsCrossfilter(annoMatrix).select(
"emb",
newEmbeddingName,
{
mode: "all",
}
);
return [annoMatrix, obsCrossfilter];
}
export const layoutChoiceAction = (newLayoutChoice) => async (
dispatch,
getState
) => {
/*
On layout choice, make sure we have selected all on the previous layout, AND the new
layout.
*/
const { annoMatrix: prevAnnoMatrix } = getState();
const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
prevAnnoMatrix,
newLayoutChoice
);
dispatch({
type: "set layout choice",
layoutChoice: newLayoutChoice,
obsCrossfilter,
annoMatrix,
});
};
client/src/actions/index.js
+23 -2
View File
@@ -12,6 +12,7 @@ import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
import * as selnActions from "./selection";
import * as annoActions from "./annotation";
import * as viewActions from "./viewStack";
import * as embActions from "./embedding";
/*
return promise fetching user-configured colors
@@ -40,6 +41,15 @@ async function configFetch(dispatch) {
});
}
function prefetchEmbeddings(annoMatrix) {
/*
prefetch requests for all embeddings
*/
const { schema } = annoMatrix;
const available = schema.layout.obs.map((v) => v.name);
available.forEach((embName) => annoMatrix.prefetch("emb", embName));
}
/*
Application bootstrap
*/
@@ -48,7 +58,7 @@ const doInitialDataLoad = () =>
dispatch({ type: "initial data load start" });
try {
const [, schema] = await Promise.all([
const [config, schema] = await Promise.all([
configFetch(dispatch),
schemaFetch(dispatch),
userColorsFetchAndLoad(dispatch),
@@ -57,12 +67,23 @@ const doInitialDataLoad = () =>
const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
prefetchEmbeddings(annoMatrix);
dispatch({
type: "annoMatrix: init complete",
annoMatrix,
obsCrossfilter,
});
dispatch({ type: "initial data load complete" });
const defaultEmbedding = config?.parameters?.["default_embedding"];
const layoutSchema = schema?.schema?.layout?.obs ?? [];
if (
defaultEmbedding &&
layoutSchema.some((s) => s.name === defaultEmbedding)
) {
dispatch(embActions.layoutChoiceAction(defaultEmbedding));
}
} catch (error) {
dispatch({ type: "initial data load error", error });
}
@@ -210,6 +231,6 @@ export default {
annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
layoutChoiceAction: selnActions.layoutChoiceAction,
layoutChoiceAction: embActions.layoutChoiceAction,
setCellSetFromSelection: selnActions.setCellSetFromSelection,
};
client/src/actions/reembed.js
+14 -21
View File
@@ -1,10 +1,10 @@
import { API } from "../globals";
import { MatrixFBS } from "../util/stateManager";
import {
postNetworkErrorToast,
postAsyncSuccessToast,
postAsyncFailureToast,
} from "../components/framework/toasters";
import { _switchEmbedding } from "./embedding";
function abortableFetch(request, opts, timeout = 0) {
const controller = new AbortController();
@@ -24,7 +24,7 @@ function abortableFetch(request, opts, timeout = 0) {
async function doReembedFetch(dispatch, getState) {
const state = getState();
let cells = state.world.obsAnnotations.rowIndex.labels();
let cells = state.annoMatrix.rowIndex.labels();
// These lines ensure that we convert any TypedArray to an Array.
// This is necessary because JSON.stringify() does some very strange
@@ -54,10 +54,7 @@ async function doReembedFetch(dispatch, getState) {
});
const res = await af.ready();
if (
res.ok &&
res.headers.get("Content-Type").includes("application/octet-stream")
) {
if (res.ok && res.headers.get("Content-Type").includes("application/json")) {
return res;
}
@@ -67,7 +64,6 @@ async function doReembedFetch(dispatch, getState) {
if (body && body.length > 0) {
msg = `${msg} -- ${body}`;
}
postNetworkErrorToast(msg);
throw new Error(msg);
}
@@ -78,17 +74,24 @@ export function requestReembed() {
return async (dispatch, getState) => {
try {
const res = await doReembedFetch(dispatch, getState);
const schema = JSON.parse(res.headers.get("CxG-Schema"));
const buffer = await res.arrayBuffer();
const df = MatrixFBS.matrixFBSToDataframe(buffer);
const schema = await res.json();
dispatch({
type: "reembed: request completed",
});
const { annoMatrix: prevAnnoMatrix } = getState();
const base = prevAnnoMatrix.base().addEmbedding(schema);
const [annoMatrix, obsCrossfilter] = await _switchEmbedding(
base,
schema.name
);
dispatch({
type: "reembed: add reembedding",
embedding: df,
schema,
annoMatrix,
obsCrossfilter,
});
postAsyncSuccessToast("Re-embedding has completed.");
} catch (error) {
dispatch({
@@ -103,13 +106,3 @@ export function requestReembed() {
}
};
}
/* disabled until reimplementation occurs
export function reembedResetWorldToUniverse(dispatch, getState) {
const { reembedController } = getState();
if (reembedController.pendingFetch) reembedController.pendingFetch.abort();
dispatch({
type: "reembed: clear all reembeddings",
});
}
*/
client/src/actions/selection.js
-25
View File
@@ -185,31 +185,6 @@ export const graphLassoEndAction = (embName, polygon) => async (
});
};
export const layoutChoiceAction = (newLayoutChoice) => async (
dispatch,
getState
) => {
/*
On layout choice, make sure we have selected all on the previous layout, AND the new
layout.
*/
const { obsCrossfilter: prevObsCrossfilter, layoutChoice } = getState();
let obsCrossfilter = await prevObsCrossfilter.select(
"emb",
layoutChoice.current,
{ mode: "all" }
);
obsCrossfilter = await obsCrossfilter.select("emb", newLayoutChoice, {
mode: "all",
});
dispatch({
type: "set layout choice",
layoutChoice: newLayoutChoice,
obsCrossfilter,
});
};
/*
Differential expression set selection
*/
client/src/actions/viewStack.js
+12 -36
View File
@@ -11,7 +11,12 @@ stack multiple subsets.
If these conventions change, code elsewhere (eg. menubar/clip.js) will need to
change as well.
*/
import { AnnoMatrixObsCrossfilter, clip, isubsetMask } from "../annoMatrix";
import { AnnoMatrixObsCrossfilter } from "../annoMatrix";
import {
_clipAnnoMatrix,
_userSubsetAnnoMatrix,
_userResetSubsetAnnoMatrix,
} from "../util/stateManager/viewStackHelpers";
export const clipAction = (min, max) => (dispatch, getState) => {
/*
@@ -19,9 +24,7 @@ export const clipAction = (min, max) => (dispatch, getState) => {
view is ALWAYS the top view.
*/
const { annoMatrix: prevAnnoMatrix } = getState();
const annoMatrix = prevAnnoMatrix.isClipped
? clip(prevAnnoMatrix.viewOf, min, max)
: clip(prevAnnoMatrix, min, max);
const annoMatrix = _clipAnnoMatrix(prevAnnoMatrix, min, max);
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
dispatch({
type: "set clip quantiles",
@@ -43,24 +46,10 @@ export const subsetAction = () => (dispatch, getState) => {
annoMatrix: prevAnnoMatrix,
obsCrossfilter: prevObsCrossfilter,
} = getState();
let annoMatrix;
if (prevAnnoMatrix.isClipped) {
// if there is a clip view, pop it and reapply after we subset
const { clipRange } = prevAnnoMatrix;
annoMatrix = isubsetMask(
prevAnnoMatrix.viewOf,
prevObsCrossfilter.allSelectedMask()
);
annoMatrix = clip(annoMatrix, ...clipRange);
} else {
// else just push a subset view.
annoMatrix = isubsetMask(
prevAnnoMatrix,
prevObsCrossfilter.allSelectedMask()
);
}
const annoMatrix = _userSubsetAnnoMatrix(
prevAnnoMatrix,
prevObsCrossfilter.allSelectedMask()
);
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
dispatch({
type: "subset to selection",
@@ -77,20 +66,7 @@ export const resetSubsetAction = () => (dispatch, getState) => {
*/
const { annoMatrix: prevAnnoMatrix } = getState();
const clipRange = prevAnnoMatrix.isClipped ? prevAnnoMatrix.clipRange : null;
/* pop all views */
let annoMatrix = prevAnnoMatrix;
while (annoMatrix.isView) {
annoMatrix = annoMatrix.viewOf;
}
/* re-apply the clip, if any */
if (clipRange !== null) {
annoMatrix = clip(annoMatrix, ...clipRange);
}
const annoMatrix = _userResetSubsetAnnoMatrix(prevAnnoMatrix);
const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
dispatch({
type: "reset subset",
client/src/annoMatrix/annoMatrix.js
+16
View File
@@ -70,6 +70,8 @@ export default class AnnoMatrix {
The row index labels are as defined by the base dataset from the server.
* isView - true if this is a view, false if not.
* viewOf - pointer to parent annomatrix if a view, undefined/null if not a view.
* userFlags - container for any additional state a user of this API wants to hang
off of an annoMatrix, and have propagated by the (shallow) cloning protocol.
*/
this.schema = indexEntireSchema(schema);
this.nObs = nObs;
@@ -77,6 +79,7 @@ export default class AnnoMatrix {
this.rowIndex = rowIndex || new IdentityInt32Index(nObs);
this.isView = false;
this.viewOf = undefined;
this.userFlags = {};
/*
Private instance variables.
@@ -394,6 +397,19 @@ export default class AnnoMatrix {
_subclassResponsibility();
}
// eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements
addEmbedding(colSchema) {
/*
Add a new obs embedding to the AnnoMatrix, with provided schema.
Returns a new annomatrix.
Typical use will be to add a re-embedding that the server has calculated.
Will throw if the column schema is invalid (eg, duplicate name).
*/
_subclassResponsibility();
}
/**
** Private interfaces below.
**/
client/src/annoMatrix/crossfilter.js
+5
View File
@@ -118,6 +118,11 @@ export default class AnnoMatrixObsCrossfilter {
return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter);
}
addEmbedding(colSchema) {
const annoMatrix = this.annoMatrix.addEmbedding(colSchema);
return new AnnoMatrixObsCrossfilter(annoMatrix, this.obsCrossfilter);
}
/**
Selection state - API is identical to ImmutableTypedCrossfilter, as these
are just wrappers to lazy create indices.
client/src/annoMatrix/loader.js
+48 -28
View File
@@ -6,6 +6,7 @@ import {
removeObsAnnoColumn,
addObsAnnoCategory,
removeObsAnnoCategory,
addObsLayout,
} from "../util/stateManager/schemaHelpers";
import { isArrayOrTypedArray } from "../util/typeHelpers";
import { _whereCacheCreate } from "./whereCache";
@@ -47,9 +48,9 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colSchema = _getColumnSchema(this.schema, "obs", col);
_writableCategoryTypeCheck(colSchema); // throws on error
const o = this._clone();
o.schema = addObsAnnoCategory(this.schema, col, category);
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, category);
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
@@ -59,13 +60,17 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colSchema = _getColumnSchema(this.schema, "obs", col);
_writableCategoryTypeCheck(colSchema); // throws on error
const o = await this.resetObsColumnValues(
const newAnnoMatrix = await this.resetObsColumnValues(
col,
category,
unassignedCategory
);
o.schema = removeObsAnnoCategory(o.schema, col, category);
return o;
newAnnoMatrix.schema = removeObsAnnoCategory(
newAnnoMatrix.schema,
col,
category
);
return newAnnoMatrix;
}
dropObsColumn(col) {
@@ -75,10 +80,10 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
const colSchema = _getColumnSchema(this.schema, "obs", col);
_writableCheck(colSchema); // throws on error
const o = this._clone();
o._cache.obs = this._cache.obs.dropCol(col);
o.schema = removeObsAnnoColumn(this.schema, col);
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col);
return newAnnoMatrix;
}
addObsColumn(colSchema, Ctor, value) {
@@ -90,15 +95,15 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
If an array, it must be of same size as nObs and same type as Ctor
*/
colSchema.writable = true;
const col = colSchema.name;
const colName = colSchema.name;
if (
_getColumnSchema(this.schema, "obs", col) ||
this._cache.obs.hasCol(col)
_getColumnSchema(this.schema, "obs", colName) ||
this._cache.obs.hasCol(colName)
) {
throw new Error("column already exists");
}
const o = this._clone();
const newAnnoMatrix = this._clone();
let data;
if (isArrayOrTypedArray(value)) {
if (value.constructor !== Ctor)
@@ -109,12 +114,13 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
} else {
data = new Ctor(this.nObs).fill(value);
}
o._cache.obs = this._cache.obs.withCol(col, data);
o.schema = addObsAnnoColumn(this.schema, col, {
...colSchema,
writable: true,
});
return o;
newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data);
_normalizeCategoricalSchema(
colSchema,
newAnnoMatrix._cache.obs.col(colName)
);
newAnnoMatrix.schema = addObsAnnoColumn(this.schema, colName, colSchema);
return newAnnoMatrix;
}
renameObsColumn(oldCol, newCol) {
@@ -157,13 +163,13 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
data[idx] = value;
}
const o = this._clone();
o._cache.obs = this._cache.obs.replaceColData(col, data);
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
const { categories } = colSchema;
if (!categories?.includes(value)) {
o.schema = addObsAnnoCategory(this.schema, col, value);
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, value);
}
return o;
return newAnnoMatrix;
}
async resetObsColumnValues(col, oldValue, newValue) {
@@ -187,13 +193,27 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
if (data[i] === oldValue) data[i] = newValue;
}
const o = this._clone();
o._cache.obs = this._cache.obs.replaceColData(col, data);
const newAnnoMatrix = this._clone();
newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data);
const { categories } = colSchema;
if (!categories?.includes(newValue)) {
o.schema = addObsAnnoCategory(this.schema, col, newValue);
newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, newValue);
}
return o;
return newAnnoMatrix;
}
addEmbedding(colSchema) {
/*
add new layout to the obs embeddings
*/
const { name: colName } = colSchema;
if (_getColumnSchema(this.schema, "emb", colName)) {
throw new Error("column already exists");
}
const newAnnoMatrix = this._clone();
newAnnoMatrix.schema = addObsLayout(this.schema, colSchema);
return newAnnoMatrix;
}
/**
client/src/annoMatrix/schema.js
+8 -2
View File
@@ -66,9 +66,14 @@ export function _isContinuousType(schema) {
export function _normalizeCategoricalSchema(colSchema, col) {
const { type, writable } = colSchema;
if (type === "string" || type === "boolean" || type === "categorical") {
if (
type === "string" ||
type === "boolean" ||
type === "categorical" ||
writable
) {
const categorySet = new Set(
col.summarize().categories.concat(colSchema.categories ?? [])
col.summarizeCategorical().categories.concat(colSchema.categories ?? [])
);
if (writable && !categorySet.has(unassignedCategoryLabel)) {
categorySet.add(unassignedCategoryLabel);
@@ -79,4 +84,5 @@ export function _normalizeCategoricalSchema(colSchema, col) {
if (colSchema.categories) {
colSchema.categories = catLabelSort(writable, colSchema.categories);
}
return colSchema;
}
client/src/annoMatrix/viewCreators.js
+8 -1
View File
@@ -33,6 +33,13 @@ export function subset(annoMatrix, obsLabels) {
return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
}
export function subsetByIndex(annoMatrix, obsIndex) {
/*
subset based upon the new obs index.
*/
return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex);
}
export function clip(annoMatrix, qmin, qmax) {
/*
Create a view that clips all continuous data to the [min, max] range.
@@ -59,5 +66,5 @@ function _maskToList(mask) {
elems += 1;
}
}
return new Int32Array(list.buffer, 0, elems);
return list.subarray(0, elems);
}
client/src/annoMatrix/views.js
+46 -31
View File
@@ -17,59 +17,74 @@ class AnnoMatrixView extends AnnoMatrix {
}
addObsAnnoCategory(col, category) {
const o = this._clone();
o.viewOf = this.viewOf.addObsAnnoCategory(col, category);
o.schema = o.viewOf.schema;
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async removeObsAnnoCategory(col, category, unassignedCategory) {
const o = this._clone();
o.viewOf = await this.viewOf.removeObsAnnoCategory(
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory(
col,
category,
unassignedCategory
);
o.schema = o.viewOf.schema;
return o;
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
dropObsColumn(col) {
const o = this._clone();
o.viewOf = this.viewOf.dropObsColumn(col);
o._cache.obs = this._cache.obs.dropCol(col);
o.schema = o.viewOf.schema;
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col);
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
addObsColumn(colSchema, Ctor, value) {
const o = this._clone();
o.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
o.schema = o.viewOf.schema;
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
renameObsColumn(oldCol, newCol) {
const o = this._clone();
o.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
o.schema = o.viewOf.schema;
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async setObsColumnValues(col, rowLabels, value) {
const o = this._clone();
o.viewOf = await this.viewOf.setObsColumnValues(col, rowLabels, value);
o._cache.obs = this._cache.obs.dropCol(col);
o.schema = o.viewOf.schema;
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues(
col,
rowLabels,
value
);
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
async resetObsColumnValues(col, oldValue, newValue) {
const o = this._clone();
o.viewOf = await this.viewOf.resetObsColumnValues(col, oldValue, newValue);
o._cache.obs = this._cache.obs.dropCol(col);
o.schema = o.viewOf.schema;
return o;
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues(
col,
oldValue,
newValue
);
newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
addEmbedding(colSchema) {
const newAnnoMatrix = this._clone();
newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema);
newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema;
return newAnnoMatrix;
}
}
client/src/components/app.js
+2
View File
@@ -11,6 +11,7 @@ import Legend from "./continuousLegend";
import Graph from "./graph/graph";
import MenuBar from "./menubar";
import Autosave from "./autosave";
import Embedding from "./embedding";
import TermsOfServicePrompt from "./termsPrompt";
import actions from "../actions";
@@ -73,6 +74,7 @@ class App extends React.Component {
{(viewportRef) => (
<>
<MenuBar />
<Embedding />
<Autosave />
<TermsOfServicePrompt />
<Legend viewportRef={viewportRef} />
client/src/components/autosave/filenameDialog.js
+4 -2
View File
@@ -13,6 +13,7 @@ import {
@connect((state) => ({
idhash: state.config?.parameters?.["annotations-user-data-idhash"] ?? null,
annotations: state.annotations,
auth: state.config?.authentication,
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
}))
class FilenameDialog extends React.Component {
@@ -90,12 +91,13 @@ class FilenameDialog extends React.Component {
};
render() {
const { writableCategoriesEnabled, annotations, idhash } = this.props;
const { writableCategoriesEnabled, annotations, idhash, auth } = this.props;
const { filenameText } = this.state;
return writableCategoriesEnabled &&
!annotations.dataCollectionNameIsReadOnly &&
!annotations.dataCollectionName ? (
!annotations.dataCollectionName &&
auth.is_authenticated ? (
<Dialog
icon="tag"
title="Annotations Collection"
client/src/components/categorical/category/index.js
+7 -3
View File
@@ -1,7 +1,7 @@
import React, { useRef, useEffect } from "react";
import { connect, shallowEqual } from "react-redux";
import { FaChevronRight, FaChevronDown } from "react-icons/fa";
import { AnchorButton, Button, Tooltip } from "@blueprintjs/core";
import { AnchorButton, Button, Tooltip, Position } from "@blueprintjs/core";
import { Flipper, Flipped } from "react-flip-toolkit";
import Async from "react-async";
import memoize from "memoize-one";
@@ -438,9 +438,13 @@ const CategoryHeader = React.memo(
? `Coloring by ${metadataField} is disabled, as it exceeds the limit of ${globals.maxCategoricalOptionsToDisplay} labels`
: "Use as color scale"
}
position="bottom"
usePortal={false}
position={Position.LEFT}
usePortal
hoverOpenDelay={globals.tooltipHoverOpenDelay}
modifiers={{
preventOverflow: { enabled: false },
hide: { enabled: false },
}}
>
<AnchorButton
data-testclass="colorby"
client/src/components/categorical/value/index.js
+3 -1
View File
@@ -453,7 +453,9 @@ class CategoryValue extends React.Component {
label,
CHART_WIDTH,
VALUE_HEIGHT
) ?? {};
) ?? {}; // if createHistogramBins returns empty object assign null to deconstructed
if (!xScale || !yScale || !bins) return null;
return (
<MiniHistogram
client/src/components/continuous/continuous.js
+1
View File
@@ -16,6 +16,7 @@ class Continuous extends React.PureComponent {
const allContinuousNames = schema.annotations.obs.columns
.filter((col) => col.type === "int32" || col.type === "float32")
.filter((col) => col.name !== obsIndex)
.filter((col) => !col.writable) // skip user annotations - they will be treated as categorical
.map((col) => col.name);
return (
client/src/components/embedding/index.js
+153
View File
@@ -0,0 +1,153 @@
import React from "react";
import { connect } from "react-redux";
import { useAsync } from "react-async";
import {
ButtonGroup,
Popover,
Button,
Radio,
RadioGroup,
Tooltip,
Position,
} from "@blueprintjs/core";
import * as globals from "../../globals";
import actions from "../../actions";
import { getDiscreteCellEmbeddingRowIndex } from "../../util/stateManager/viewStackHelpers";
@connect((state) => {
return {
layoutChoice: state.layoutChoice, // TODO: really should clean up naming, s/layout/embedding/g
schema: state.annoMatrix?.schema,
crossfilter: state.obsCrossfilter,
};
})
class Embedding extends React.PureComponent {
constructor(props) {
super(props);
this.state = {};
}
handleLayoutChoiceChange = (e) => {
const { dispatch } = this.props;
dispatch(actions.layoutChoiceAction(e.currentTarget.value));
};
render() {
const { layoutChoice, schema, crossfilter } = this.props;
const { annoMatrix } = crossfilter;
return (
<ButtonGroup
style={{
position: "absolute",
display: "inherit",
left: 8,
bottom: 8,
zIndex: 9999,
}}
>
<Popover
target={
<Tooltip
content="Select embedding for visualization"
position="top"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<Button
type="button"
data-testid="layout-choice"
icon="heatmap"
// minimal
id="embedding"
style={{
cursor: "pointer",
}}
>
{layoutChoice?.current}: {crossfilter.countSelected()} out of{" "}
{crossfilter.size()} cells
</Button>
</Tooltip>
}
// minimal /* removes arrow */
position={Position.TOP_LEFT}
content={
<div
style={{
display: "flex",
justifyContent: "flex-start",
alignItems: "flex-start",
flexDirection: "column",
padding: 10,
width: 400,
}}
>
<h1>Embedding Choice</h1>
<p style={{ fontStyle: "italic" }}>
There are {schema?.dataframe?.nObs} cells in the entire dataset.
</p>
<EmbeddingChoices
onChange={this.handleLayoutChoiceChange}
annoMatrix={annoMatrix}
layoutChoice={layoutChoice}
/>
</div>
}
/>
</ButtonGroup>
);
}
}
export default Embedding;
const loadAllEmbeddingCounts = async ({ annoMatrix, available }) => {
const embeddings = await Promise.all(
available.map((name) => annoMatrix.base().fetch("emb", name))
);
return available.map((name, idx) => ({
embeddingName: name,
embedding: embeddings[idx],
discreteCellIndex: getDiscreteCellEmbeddingRowIndex(embeddings[idx]),
}));
};
const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
const { available } = layoutChoice;
const { data, error, isPending } = useAsync({
promiseFn: loadAllEmbeddingCounts,
annoMatrix,
available,
});
if (error) {
/* log, as this is unexpected */
console.error(error);
}
if (error || isPending) {
/* still loading, or errored out - just omit counts (TODO: spinner?) */
return (
<RadioGroup onChange={onChange} selectedValue={layoutChoice.current}>
{layoutChoice.available.map((name) => (
<Radio label={`${name}`} value={name} key={name} />
))}
</RadioGroup>
);
}
if (data) {
return (
<RadioGroup onChange={onChange} selectedValue={layoutChoice.current}>
{data.map((summary) => {
const { discreteCellIndex, embeddingName } = summary;
const sizeHint = `${discreteCellIndex.size()} cells`;
return (
<Radio
label={`${embeddingName}: ${sizeHint}`}
value={embeddingName}
key={embeddingName}
/>
);
})}
</RadioGroup>
);
}
return null;
};
client/src/components/graph/graph.js
+5 -3
View File
@@ -34,8 +34,10 @@ function createProjectionTF(viewportWidth, viewportHeight) {
the projection transform accounts for the screen size & other layout
*/
const fractionToUse = 0.95; // fraction of min dimension to use
const topGutterSizePx = 32; // toolbar box height
const heightMinusGutter = viewportHeight - topGutterSizePx;
const topGutterSizePx = 32; // top gutter for tools
const bottomGutterSizePx = 32; // bottom gutter for tools
const heightMinusGutter =
viewportHeight - topGutterSizePx - bottomGutterSizePx;
const minDim = Math.min(viewportWidth, heightMinusGutter);
const aspectScale = [
(fractionToUse * minDim) / viewportWidth,
@@ -44,7 +46,7 @@ function createProjectionTF(viewportWidth, viewportHeight) {
const m = mat3.create();
mat3.fromTranslation(m, [
0,
-topGutterSizePx / viewportHeight / aspectScale[1],
(bottomGutterSizePx - topGutterSizePx) / viewportHeight / aspectScale[1],
]);
mat3.scale(m, m, aspectScale);
return m;
client/src/components/menubar/authButtons.js
+32
View File
@@ -0,0 +1,32 @@
import React from "react";
import { AnchorButton, Tooltip } from "@blueprintjs/core";
import * as globals from "../../globals";
import styles from "./menubar.css";
const Auth = React.memo((props) => {
const { auth } = props;
if (!auth || (auth && !auth.requires_client_login)) return null;
return (
<div className={`bp3-button-group ${styles.menubarButton}`}>
<Tooltip
content="Log in or log out of cellxgene"
position="bottom"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<AnchorButton
type="button"
data-testid="auth-button"
disabled={false}
icon={!auth.is_authenticated ? "log-in" : "log-out"}
href={!auth.is_authenticated ? auth.login : auth.logout}
>
{!auth.is_authenticated ? "Log In" : "Log Out"}
</AnchorButton>
</Tooltip>
</div>
);
});
export default Auth;
client/src/components/menubar/embedding.js
-118
View File
@@ -1,118 +0,0 @@
import React from "react";
import {
ButtonGroup,
Popover,
Button,
Radio,
RadioGroup,
Tooltip,
Position,
} from "@blueprintjs/core";
import { connect } from "react-redux";
import * as globals from "../../globals";
import styles from "./menubar.css";
import actions from "../../actions";
@connect((state) => ({
layoutChoice: state.layoutChoice,
// disabled temporarily. TODO - issue #1606
// reembedController: state.reembedController,
// enableReembedding: state.config?.parameters?.["enable-reembedding"] ?? false,
enableReembedding: false,
}))
class Embedding extends React.PureComponent {
handleLayoutChoiceChange = (e) => {
const { dispatch } = this.props;
dispatch(actions.layoutChoiceAction(e.currentTarget.value));
};
// eslint-disable-next-line class-methods-use-this -- temporary disable
renderReembedding() {
return null;
/* disabled pending rewrite. TODO - issue #1606
const {
enableReembedding,
world,
universe,
dispatch,
reembedController,
} = this.props;
if (!enableReembedding) return null;
const loading = !!reembedController?.pendingFetch;
const disabled = World.worldEqUniverse(world, universe);
const tipContent = disabled
? "Subset cells first, then click to recompute UMAP embedding."
: "Click to recompute UMAP embedding on the current cell subset.";
return (
<Tooltip
content={tipContent}
position="bottom"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<AnchorButton
icon="new-object"
style={{ marginRight: 10 }}
disabled={disabled}
onClick={() => dispatch(actions.requestReembed())}
loading={loading}
/>
</Tooltip>
);
*/
}
render() {
const { layoutChoice } = this.props;
return (
<ButtonGroup className={styles.menubarButton}>
<Popover
target={
<Tooltip
content="Select embedding for visualization"
position="bottom"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<Button
type="button"
data-testid="layout-choice"
icon="heatmap"
style={{
cursor: "pointer",
}}
/>
</Tooltip>
}
position={Position.BOTTOM_RIGHT}
content={
<div
style={{
display: "flex",
justifyContent: "flex-start",
alignItems: "flex-start",
flexDirection: "column",
padding: 10,
}}
>
<RadioGroup
label="Embedding Choice"
onChange={this.handleLayoutChoiceChange}
selectedValue={layoutChoice.current}
>
{layoutChoice.available.map((name) => (
<Radio label={name} value={name} key={name} />
))}
</RadioGroup>
</div>
}
/>
{this.renderReembedding()}
</ButtonGroup>
);
}
}
export default Embedding;
client/src/components/menubar/index.js
+15 -5
View File
@@ -6,11 +6,13 @@ import * as globals from "../../globals";
import styles from "./menubar.css";
import actions from "../../actions";
import Clip from "./clip";
import Embedding from "./embedding";
import AuthButtons from "./authButtons";
import InformationMenu from "./infoMenu";
import Subset from "./subset";
import UndoRedoReset from "./undoRedo";
import DiffexpButtons from "./diffexpButtons";
import Reembedding from "./reembedding";
import { getEmbSubsetView } from "../../util/stateManager/viewStackHelpers";
@connect((state) => {
const { annoMatrix } = state;
@@ -18,9 +20,11 @@ import DiffexpButtons from "./diffexpButtons";
const selectedCount = crossfilter.countSelected();
const subsetPossible =
selectedCount !== 0 && selectedCount !== crossfilter.size(); // ie, not all are selected
const subsetResetPossible =
annoMatrix.nObs !== annoMatrix.schema.dataframe.nObs;
selectedCount !== 0 && selectedCount !== crossfilter.size(); // ie, not all and not none are selected
const embSubsetView = getEmbSubsetView(annoMatrix);
const subsetResetPossible = !embSubsetView
? annoMatrix.nObs !== annoMatrix.schema.dataframe.nObs
: annoMatrix.nObs !== embSubsetView.nObs;
return {
subsetPossible,
@@ -37,6 +41,7 @@ import DiffexpButtons from "./diffexpButtons";
celllist1: state.differential.celllist1,
celllist2: state.differential.celllist2,
libraryVersions: state.config?.["library_versions"],
auth: state.config?.authentication,
undoDisabled: state["@@undoable/past"].length === 0,
redoDisabled: state["@@undoable/future"].length === 0,
aboutLink: state.config?.links?.["about-dataset"],
@@ -47,6 +52,8 @@ import DiffexpButtons from "./diffexpButtons";
tosURL: state.config?.parameters?.["about_legal_tos"],
privacyURL: state.config?.parameters?.["about_legal_privacy"],
categoricalSelection: state.categoricalSelection,
enableReembedding:
state.config?.parameters?.["enable-reembedding"] ?? false,
};
})
class MenuBar extends React.PureComponent {
@@ -212,6 +219,8 @@ class MenuBar extends React.PureComponent {
colorAccessor,
subsetPossible,
subsetResetPossible,
enableReembedding,
auth,
} = this.props;
const { pendingClipPercentiles } = this.state;
@@ -237,6 +246,7 @@ class MenuBar extends React.PureComponent {
zIndex: 3,
}}
>
<AuthButtons auth={auth} />
<InformationMenu
libraryVersions={libraryVersions}
aboutLink={aboutLink}
@@ -264,7 +274,7 @@ class MenuBar extends React.PureComponent {
this.handleClipPercentileMinValueChange
}
/>
<Embedding />
{enableReembedding ? <Reembedding /> : null}
<Tooltip
content="When a category is colored by, show labels on the graph"
position="bottom"
client/src/components/menubar/reembedding.js
+40
View File
@@ -0,0 +1,40 @@
import React from "react";
import { connect } from "react-redux";
import { AnchorButton, ButtonGroup, Tooltip } from "@blueprintjs/core";
import * as globals from "../../globals";
import actions from "../../actions";
import styles from "./menubar.css";
@connect((state) => ({
reembedController: state.reembedController,
annoMatrix: state.annoMatrix,
}))
class Reembedding extends React.PureComponent {
render() {
const { dispatch, annoMatrix, reembedController } = this.props;
const loading = !!reembedController?.pendingFetch;
const disabled = annoMatrix.nObs === annoMatrix.schema.dataframe.nObs;
const tipContent = disabled
? "Subset cells first, then click to recompute UMAP embedding."
: "Click to recompute UMAP embedding on the current cell subset.";
return (
<ButtonGroup className={styles.menubarButton}>
<Tooltip
content={tipContent}
position="bottom"
hoverOpenDelay={globals.tooltipHoverOpenDelay}
>
<AnchorButton
icon="new-object"
disabled={disabled}
onClick={() => dispatch(actions.requestReembed())}
loading={loading}
/>
</Tooltip>
</ButtonGroup>
);
}
}
export default Reembedding;
client/src/components/miniHistogram/index.js
+3 -2
View File
@@ -40,10 +40,11 @@ export default class MiniHistogram extends React.PureComponent {
};
componentDidUpdate = (prevProps) => {
const { obsOrVarContinuousFieldDisplayName } = this.props;
const { obsOrVarContinuousFieldDisplayName, bins } = this.props;
if (
prevProps.obsOrVarContinuousFieldDisplayName !==
obsOrVarContinuousFieldDisplayName
obsOrVarContinuousFieldDisplayName ||
prevProps.bins !== bins
)
this.drawHistogram();
};
client/src/components/scatterplot/scatterplot.js
+19 -8
View File
@@ -438,18 +438,19 @@ class Scatterplot extends React.PureComponent {
pointDilation,
} = this.props;
const { minimized, regl, viewport } = this.state;
const bottomToolbarGutter = 48; // gutter for bottom tool bar
return (
<div
style={{
position: "fixed",
bottom: minimized ? -height + -margin.top - 2 : 0,
bottom: bottomToolbarGutter,
borderRadius: "3px 3px 0px 0px",
left: globals.leftSidebarWidth + globals.scatterplotMarginLeft,
padding: "0px 20px 20px 0px",
background: "white",
/* x y blur spread color */
boxShadow: "0px 0px 6px 2px rgba(153,153,153,0.4)",
boxShadow: "0px 0px 3px 2px rgba(153,153,153,0.2)",
zIndex: 2,
}}
id="scatterplot_wrapper"
@@ -488,7 +489,9 @@ class Scatterplot extends React.PureComponent {
id="scatterplot"
style={{
width: `${width + margin.left + margin.right}px`,
height: `${height + margin.top + margin.bottom}px`,
height: `${
(minimized ? 0 : height + margin.top) + margin.bottom
}px`,
}}
>
<canvas
@@ -498,6 +501,7 @@ class Scatterplot extends React.PureComponent {
style={{
marginLeft: margin.left,
marginTop: margin.top,
display: minimized ? "none" : null,
}}
ref={this.setReglCanvas}
/>
@@ -523,9 +527,7 @@ class Scatterplot extends React.PureComponent {
}
return (
<ScatterplotAxis
width={width}
height={height}
margin={margin}
minimized={minimized}
scatterplotYYaccessor={scatterplotXXaccessor}
scatterplotXXaccessor={scatterplotYYaccessor}
xScale={asyncProps.xScale}
@@ -544,7 +546,13 @@ class Scatterplot extends React.PureComponent {
export default Scatterplot;
const ScatterplotAxis = React.memo(
({ scatterplotYYaccessor, scatterplotXXaccessor, xScale, yScale }) => {
({
minimized,
scatterplotYYaccessor,
scatterplotXXaccessor,
xScale,
yScale,
}) => {
/*
Axis for the scatterplot, rendered with SVG/D3. Props:
* scatterplotXXaccessor - name of X axis
@@ -559,7 +567,7 @@ const ScatterplotAxis = React.memo(
const svgRef = useRef(null);
useEffect(() => {
if (!svgRef.current) return;
if (!svgRef.current || minimized) return;
const svg = d3.select(svgRef.current);
svg.selectAll("*").remove();
@@ -608,6 +616,9 @@ const ScatterplotAxis = React.memo(
width={width + margin.left + margin.right}
height={height + margin.top + margin.bottom}
data-testid="scatterplot-svg"
style={{
display: minimized ? "none" : null,
}}
>
<g ref={svgRef} transform={`translate(${margin.left},${margin.top})`} />
</svg>
client/src/globals.js
+1 -1
View File
@@ -61,7 +61,7 @@ export const maxControlsWidth = 800;
export const graphMargin = { top: 20, right: 10, bottom: 30, left: 40 };
export const graphWidth = 700;
export const graphHeight = 700;
export const scatterplotMarginLeft = 25;
export const scatterplotMarginLeft = 11;
export const rightSidebarWidth = 365;
export const leftSidebarWidth = 365;
client/src/index.js
-1
View File
@@ -1,4 +1,3 @@
// jshint esversion: 6
import React from "react";
import ReactDOM from "react-dom";
import { Provider } from "react-redux";
client/src/reducers/continuousSelection.js
+1
View File
@@ -3,6 +3,7 @@ import { makeContinuousDimensionName } from "../util/nameCreators";
const ContinuousSelection = (state = {}, action) => {
switch (action.type) {
case "reset subset":
case "subset to selection":
case "set clip quantiles": {
return {};
}
client/src/reducers/graphSelection.js
+1
View File
@@ -7,6 +7,7 @@ const GraphSelection = (
) => {
switch (action.type) {
case "set clip quantiles":
case "subset to selection":
case "reset subset":
case "set layout choice": {
return {
client/src/reducers/index.js
+1 -3
View File
@@ -18,7 +18,7 @@ import autosave from "./autosave";
import ontology from "./ontology";
import centroidLabels from "./centroidLabels";
import pointDialation from "./pointDilation";
import { reembedController, reembedding } from "./reembed";
import { reembedController } from "./reembed";
import { gcMiddleware as annoMatrixGC } from "../annoMatrix";
import undoableConfig from "./undoableConfig";
@@ -30,7 +30,6 @@ const Reducer = undoable(
["obsCrossfilter", obsCrossfilter],
["ontology", ontology],
["annotations", annotations],
["reembedding", reembedding],
["layoutChoice", layoutChoice],
["categoricalSelection", categoricalSelection],
["continuousSelection", continuousSelection],
@@ -55,7 +54,6 @@ const Reducer = undoable(
"layoutChoice",
"centroidLabels",
"annotations",
"reembedding",
],
undoableConfig
);
client/src/reducers/layoutChoice.js
+4 -16
View File
@@ -48,27 +48,15 @@ const LayoutChoice = (
}
case "reembed: add reembedding": {
const { schema } = nextSharedState.annoMatrix;
const { name } = action.schema;
const available = Array.from(new Set(state.available).add(name));
const currentDimNames = schema.layout.obsByName[name].dims;
return {
...state,
available,
};
}
case "reembed: clear all reembeddings": {
const { annoMatrix } = nextSharedState;
const { current } = state;
const dflt = setToDefaultLayout(annoMatrix.schema);
if (dflt.available.includes(current)) {
return {
...state,
available: dflt.available,
};
}
return {
...state,
...dflt,
current: name,
currentDimNames,
};
}
client/src/reducers/reembed.js
-35
View File
@@ -27,38 +27,3 @@ export const reembedController = (
}
}
};
/*
actual reembedding data is part of the undo/redo history
*/
export const reembedding = (
state = {
reembeddings: new Map(),
},
action
) => {
switch (action.type) {
case "reembed: add reembedding": {
const { schema, embedding } = action;
const { name } = schema.name;
const { reembeddings } = state;
return {
...state,
reembeddings: new Map(reembeddings).set(name, {
name,
schema,
embedding,
}),
};
}
case "reembed: clear all reembeddings": {
return {
...state,
reembeddings: new Map(),
};
}
default: {
return state;
}
}
};
client/src/util/stateManager/controlsHelpers.js
+6 -1
View File
@@ -64,7 +64,12 @@ function topNCategories(colSchema, summary, N) {
export function isSelectableCategoryName(schema, name) {
const { index } = schema.annotations.obs;
return name && name !== index && isCategoricalAnnotation(schema, name);
const colSchema = schema.annotations.obsByName[name];
return (
name &&
name !== index &&
(isCategoricalAnnotation(schema, name) || colSchema.writable)
);
}
export function selectableCategoryNames(schema, names) {
client/src/util/stateManager/matrix.js
+2 -2
View File
@@ -170,11 +170,11 @@ export function encodeMatrixFBS(df) {
function promoteTypedArray(o) {
/*
Decide what internal data type to use for the data returned from
Decide what internal data type to use for the data returned from
the server.
TODO - future optimization: not all int32/uint32 data series require
promotion to float64. We COULD simply look at the data to decide.
promotion to float64. We COULD simply look at the data to decide.
*/
if (isFpTypedArray(o) || Array.isArray(o)) return o;
client/src/util/stateManager/viewStackHelpers.js
+175
View File
@@ -0,0 +1,175 @@
/*
The annoMatrix view stack has a set of conventions which are assumed elsewhere in the
application. These helper functions make it simple for action creators to manage
the stack.
The annoMatrix module does not care about this order, but we maintain it as
a convention to make it simpler to manipulate the views.
Terminology:
- clip view: AnnoMatrixClipView
- subset view: AnnoMatrixRowSubsetView
- user subset view: create by the user explicitly subsetting by selection
- embedding subset view: implicitly created by switching the current embedding
- loader, or base annoMatrix: the root, which loads data
Rules:
1. there will be zero or one clip view
2. there will be zero or more subset views
3. there will be zero or one embedding view
4. there will be one loader/base, which is always the bottom view
5. the view ordering MUST be (top to bottom):
[clip] -> [user subset] -> [embedding subset] -> loader
There is code elsewhere in the app (eg, menubar/clip.js) which assumes this order.
Views can be interogated for their type with the following:
* is a view: annoMatrix.isView
* is the loader: !anonMatrix.isView (or annoMatrix === annoMatrix.base())
* is a clip view: annoMatrix.isClipped (or annoMatrix.clipRange)
* is a subset view: (annoMatrix.isView && !annoMatrix.isClipped)
* is a user subset view: annoMatrix.userFlags?.isUserSubsetView
* is an embedding subset view: annomatrix.userFlags?.isEmbSubsetView
*/
import { clip, isubsetMask, isubset } from "../../annoMatrix";
import { memoize } from "../dataframe/util";
export function _clipAnnoMatrix(annoMatrix, min, max) {
/*
clip the annoMatrix.
*/
return annoMatrix.isClipped
? clip(annoMatrix.viewOf, min, max)
: clip(annoMatrix, min, max);
}
export function _userSubsetAnnoMatrix(annoMatrix, mask) {
/*
user-requested row subset of annoMatrix, to be added on top of any
other previous row subsets.
*/
const { clipRange } = annoMatrix;
if (clipRange) {
annoMatrix = annoMatrix.viewOf;
}
annoMatrix = isubsetMask(annoMatrix, mask);
annoMatrix.userFlags.isUserSubsetView = true;
if (clipRange) {
annoMatrix = clip(annoMatrix, ...clipRange);
}
return annoMatrix;
}
export function _userResetSubsetAnnoMatrix(annoMatrix) {
/*
Reset/remove all user-requested subsets. Do not remove clip or embedding subset.
*/
/* stash clipping info, if any */
const { clipRange } = annoMatrix;
if (clipRange) {
annoMatrix = annoMatrix.viewOf;
}
/* pop all views except embedding subset and loader */
while (annoMatrix.isView && annoMatrix.userFlags.isUserSubsetView) {
annoMatrix = annoMatrix.viewOf;
}
/* re-apply the clip, if any */
if (clipRange) {
annoMatrix = clip(annoMatrix, ...clipRange);
}
return annoMatrix;
}
export function _setEmbeddingSubset(annoMatrix, embeddingDf) {
/*
Set the embedding subset view. Only create a subset view for the embedding
when it is needed, ie, there are NaN values in the embeddings.
*/
const embRowOffsets = _getEmbeddingRowOffsets(
annoMatrix.rowIndex,
embeddingDf
);
const curEmbSubsetView = getEmbSubsetView(annoMatrix);
/* if no current embedding subset, and no new embedding subset, just noop */
if (!embRowOffsets && !curEmbSubsetView) return annoMatrix;
// ... otherwise, do the work
/* stash clipping info, if any */
const clipRange = annoMatrix.isClipped ? annoMatrix.clipRange : null;
/* pop all subsets, user or embedding */
while (annoMatrix.isView) {
annoMatrix = annoMatrix.viewOf;
}
/* apply new embedding row index, if needed */
if (embRowOffsets) {
annoMatrix = isubset(annoMatrix, embRowOffsets);
annoMatrix.userFlags.isEmbSubsetView = true;
}
/* re-apply clip, if needed */
if (clipRange) {
annoMatrix = clip(annoMatrix, ...clipRange);
}
return annoMatrix;
}
function _getEmbeddingRowOffsets(baseRowIndex, embeddingDf) {
/*
given a dataframe containing an embedding:
- if the embedding contains no NaN coordinates, return null
- if the embedding contains NaN coordinates, return a rowIndex
that contains only the rows with discrete valued coordinates.
Currently assumes that there will be onl two dimensions in the embedding.
*/
const X = embeddingDf.icol(0).asArray();
const Y = embeddingDf.icol(1).asArray();
const offsets = new Int32Array(X.length);
let numOffsets = 0;
for (let i = 0, l = X.length; i < l; i += 1) {
if (!Number.isNaN(X[i]) && !Number.isNaN(Y[i])) {
offsets[numOffsets] = i;
numOffsets += 1;
}
}
if (numOffsets === X.length) return null;
return offsets.subarray(0, numOffsets);
}
export function _getDiscreteCellEmbeddingRowIndex(embeddingDf) {
const idx = _getEmbeddingRowOffsets(embeddingDf.rowIndex, embeddingDf);
if (idx === null) return embeddingDf.rowIndex;
return embeddingDf.rowIndex.isubset(idx);
}
export const getDiscreteCellEmbeddingRowIndex = memoize(
_getDiscreteCellEmbeddingRowIndex,
(df) => df.__id
);
export function getEmbSubsetView(annoMatrix) {
/* if there is an embedding subset in the view stack, return it. Falsish if not. */
while (annoMatrix.isView) {
if (annoMatrix.userFlags.isEmbSubsetView) return annoMatrix;
annoMatrix = annoMatrix.viewOf;
}
return undefined;
}