fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-22 06:18:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

Graph/scatterplot improvements (#893)

Browse Source 
* many graph/scatterplot fixes: 722, 882, 758, 886

* fix e2e test breakage caused by graph transform work

* convert webgl point shaders to use flags rather than explicit point size

* remove unused packages from dependencies

* fix typo in regl prop name

* factor common code into util helper file

* legibility tweaks
This commit is contained in:
Bruce Martin
2019-08-22 20:56:05 -07:00
committed by GitHub
parent 28c4d28308
commit 0f36b49840
9 changed files with 708 additions and 536 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/src/components/scatterplot/scatterplot.js
+172 -129
View File
@@ -1,43 +1,40 @@
// jshint esversion: 6
// https://bl.ocks.org/Jverma/076377dd0125b1a508621441752735fc
// https://peterbeshai.com/scatterplot-in-d3-with-voronoi-interaction.html
import React from "react";
import { connect } from "react-redux";
import { Button, ButtonGroup } from "@blueprintjs/core";
import _regl from "regl";
import * as d3 from "d3";
import { mat3 } from "gl-matrix";
import memoize from "memoize-one";
import { isTypedArray } from "../../util/typeHelpers";
import * as globals from "../../globals";
import _camera from "../../util/camera";
import setupScatterplot from "./setupScatterplot";
import styles from "./scatterplot.css";
import _drawPoints from "./drawPointsRegl";
import scaleLinear from "../../util/scaleLinear";
import { margin, width, height } from "./util";
import finiteExtent from "../../util/finiteExtent";
function createProjectionTF(viewportWidth, viewportHeight) {
/*
the projection transform accounts for the screen size & other layout
*/
const m = mat3.create();
return mat3.projection(m, viewportWidth, viewportHeight);
}
@connect(state => {
const { world, crossfilter } = state;
const { world, crossfilter, universe } = state;
const { scatterplotXXaccessor, scatterplotYYaccessor } = state.controls;
const expressionX =
world &&
scatterplotXXaccessor &&
world.varData.hasCol(scatterplotXXaccessor)
? world.varData.col(scatterplotXXaccessor).asArray()
: null;
world.varData.col(scatterplotXXaccessor)?.asArray();
const expressionY =
world &&
scatterplotYYaccessor &&
world.varData.hasCol(scatterplotYYaccessor)
? world.varData.col(scatterplotYYaccessor).asArray()
: null;
world.varData.col(scatterplotYYaccessor)?.asArray();
return {
world,
universe,
colorRGB: state.colors.rgb,
colorScale: state.colors.scale,
@@ -57,6 +54,64 @@ import finiteExtent from "../../util/finiteExtent";
};
})
class Scatterplot extends React.Component {
computePointPositions = memoize((X, Y, xScale, yScale) => {
const positions = new Float32Array(2 * X.length);
for (let i = 0, len = X.length; i < len; i += 1) {
positions[2 * i] = xScale(X[i]);
positions[2 * i + 1] = yScale(Y[i]);
}
return positions;
});
computePointColors = memoize(rgb => {
/*
compute webgl colors for each point
*/
const colors = new Float32Array(3 * rgb.length);
for (let i = 0, len = rgb.length; i < len; i += 1) {
colors.set(rgb[i], 3 * i);
}
return colors;
});
computeSelectedFlags = memoize(
(crossfilter, flagSelected, flagUnselected) => {
const x = crossfilter.fillByIsSelected(
new Float32Array(crossfilter.size()),
flagSelected,
flagUnselected
);
return x;
}
);
computePointFlags = memoize((world, crossfilter, colorAccessor) => {
const flagSelected = 1;
const flagNaN = 2;
// XXX - coming soon.
// const flagHighlight = 4;
const flags = this.computeSelectedFlags(
crossfilter,
flagSelected,
0
).slice();
const colorByColumn = colorAccessor
? world.obsAnnotations.col(colorAccessor)?.asArray() ||
world.varData.col(colorAccessor)?.asArray()
: null;
const colorByData =
colorByColumn && isTypedArray(colorByColumn) ? colorByColumn : null;
if (colorByData) {
for (let i = 0, len = flags.length; i < len; i += 1) {
flags[i] += Number.isFinite(colorByData[i]) ? 0 : flagNaN;
}
}
return flags;
});
constructor(props) {
super(props);
this.count = 0;
@@ -64,7 +119,7 @@ class Scatterplot extends React.Component {
this.renderCache = {
positions: null,
colors: null,
sizes: null,
flags: null,
xScale: null,
yScale: null
};
@@ -85,39 +140,37 @@ class Scatterplot extends React.Component {
this.renderCache = { ...this.renderCache, ...scales };
}
const camera = _camera(this.reglCanvas, { scale: true, rotate: false });
const regl = _regl(this.reglCanvas);
const drawPoints = _drawPoints(regl);
// Create render transform
const projectionTF = createProjectionTF(
this.reglCanvas.width,
this.reglCanvas.height
);
// preallocate buffers
const pointBuffer = regl.buffer();
const colorBuffer = regl.buffer();
const sizeBuffer = regl.buffer();
const flagBuffer = regl.buffer();
const reglRender = regl.frame(() => {
this.reglDraw(
regl,
drawPoints,
sizeBuffer,
colorBuffer,
pointBuffer,
camera
);
camera.tick();
});
this.reglRenderState = "rendering";
this.renderPoints(
regl,
drawPoints,
flagBuffer,
colorBuffer,
pointBuffer,
projectionTF
);
this.setState({
regl,
sizeBuffer,
flagBuffer,
pointBuffer,
colorBuffer,
svg,
reglRender,
camera,
drawPoints
drawPoints,
projectionTF
});
}
@@ -129,22 +182,22 @@ class Scatterplot extends React.Component {
scatterplotYYaccessor,
expressionX,
expressionY,
colorRGB
colorRGB,
colorAccessor
} = this.props;
const {
reglRender,
regl,
pointBuffer,
colorBuffer,
sizeBuffer,
flagBuffer,
svg,
drawPoints,
camera
projectionTF
} = this.state;
if (
scatterplotXXaccessor !== prevProps.scatterplotXXaccessor || // was CLU now FTH1 etc
scatterplotYYaccessor !== prevProps.scatterplotYYaccessor || // was CLU now FTH1 etc
scatterplotXXaccessor !== prevProps.scatterplotXXaccessor ||
scatterplotYYaccessor !== prevProps.scatterplotYYaccessor ||
world !== prevProps.world // shape or clip of world changed
) {
const scales = Scatterplot.setupScales(expressionX, expressionY);
@@ -152,76 +205,54 @@ class Scatterplot extends React.Component {
this.renderCache = { ...this.renderCache, ...scales };
}
if (reglRender && this.reglRenderState === "rendering") {
reglRender.cancel();
this.reglRenderState = "paused";
}
if (
world &&
regl &&
pointBuffer &&
colorBuffer &&
sizeBuffer &&
expressionX &&
expressionY &&
scatterplotXXaccessor &&
scatterplotYYaccessor
) {
if (world && regl) {
const { renderCache } = this;
const { xScale, yScale } = this.renderCache;
const cellCount = expressionX.length;
let needsRepaint = false;
// Points change when expressionX or expressionY change.
if (
!renderCache.positions ||
expressionX !== prevProps.expressionX ||
expressionY !== prevProps.expressionY
) {
if (!renderCache.positions) {
renderCache.positions = new Float32Array(2 * cellCount);
}
const glScaleX = scaleLinear([0, width], [-0.95, 0.95]);
const glScaleY = scaleLinear([0, height], [-1, 1]);
for (let i = 0, { positions } = renderCache; i < cellCount; i += 1) {
positions[2 * i] = glScaleX(xScale(expressionX[i]));
positions[2 * i + 1] = glScaleY(yScale(expressionY[i]));
}
pointBuffer({ data: renderCache.positions, dimension: 2 });
}
// Colors for each point - change only when props.colorsRGB change.
if (!renderCache.colors || colorRGB !== prevProps.colorRGB) {
if (!renderCache.colors) {
renderCache.colors = new Float32Array(3 * cellCount);
}
for (let i = 0, { colors } = renderCache; i < cellCount; i += 1) {
colors.set(colorRGB[i], 3 * i);
}
colorBuffer({ data: renderCache.colors, dimension: 3 });
}
// Sizes for each point - updates are triggered only when selected
// obs change
if (!renderCache.sizes || crossfilter !== prevProps.crossfilter) {
if (!renderCache.sizes) {
renderCache.sizes = new Float32Array(cellCount);
}
crossfilter.fillByIsSelected(renderCache.sizes, 4, 0.2);
sizeBuffer({ data: renderCache.sizes, dimension: 1 });
}
this.count = cellCount;
regl._refresh();
this.reglDraw(
regl,
drawPoints,
sizeBuffer,
colorBuffer,
pointBuffer,
camera
const newPositions = this.computePointPositions(
expressionX,
expressionY,
xScale,
yScale
);
if (renderCache.positions !== newPositions) {
renderCache.positions = newPositions;
pointBuffer({ data: renderCache.positions, dimension: 2 });
needsRepaint = true;
}
/* colors for each point */
const newColors = this.computePointColors(colorRGB);
if (renderCache.colors !== newColors) {
renderCache.colors = newColors;
colorBuffer({ data: renderCache.colors, dimension: 3 });
needsRepaint = true;
}
const newFlags = this.computePointFlags(
world,
crossfilter,
colorAccessor
);
if (renderCache.flags !== newFlags) {
renderCache.flags = newFlags;
flagBuffer({ data: renderCache.flags, dimension: 1 });
needsRepaint = true;
}
this.count = expressionX.length;
if (needsRepaint) {
this.renderPoints(
regl,
drawPoints,
flagBuffer,
colorBuffer,
pointBuffer,
projectionTF
);
}
}
}
@@ -241,22 +272,6 @@ class Scatterplot extends React.Component {
};
}
reglDraw(regl, drawPoints, sizeBuffer, colorBuffer, pointBuffer, camera) {
regl.clear({
depth: 1,
color: [1, 1, 1, 1]
});
drawPoints({
size: sizeBuffer,
distance: camera.distance,
color: colorBuffer,
position: pointBuffer,
count: this.count,
view: camera.view()
});
}
drawAxesSVG(xScale, yScale, svg) {
const { scatterplotYYaccessor, scatterplotXXaccessor } = this.props;
svg.selectAll("*").remove();
@@ -307,6 +322,34 @@ class Scatterplot extends React.Component {
.text(scatterplotXXaccessor);
}
renderPoints(
regl,
drawPoints,
flagBuffer,
colorBuffer,
pointBuffer,
projectionTF
) {
if (!this.reglCanvas) return;
const { universe } = this.props;
const { width: cvWidth, height: cvHeight } = this.reglCanvas;
regl.poll();
regl.clear({
depth: 1,
color: [1, 1, 1, 1]
});
drawPoints({
flag: flagBuffer,
color: colorBuffer,
position: pointBuffer,
projection: projectionTF,
count: this.count,
nPoints: universe.nObs,
minViewportDimension: Math.min(cvWidth || width, cvHeight || height)
});
regl._gl.flush();
}
render() {
const { dispatch } = this.props;
const { minimized } = this.state;
@@ -367,7 +410,7 @@ class Scatterplot extends React.Component {
height={height}
data-testid="scatterplot"
style={{
marginLeft: margin.left - 7,
marginLeft: margin.left,
marginTop: margin.top
}}
ref={canvas => {