@vitessce/all 2.0.3-beta.0 → 2.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/deflate.8ace1ac4.mjs +13 -0
- package/dist/hglib.1f1ea875.mjs +130303 -0
- package/dist/index.7dac8670.mjs +244127 -0
- package/dist/index.mjs +11 -0
- package/dist/jpeg.c8011e3a.mjs +840 -0
- package/dist/lerc.ccda5eb2.mjs +1935 -0
- package/dist/lzw.39876143.mjs +128 -0
- package/dist/packbits.9e95d117.mjs +30 -0
- package/dist/pako.esm.4b234125.mjs +3940 -0
- package/dist/raw.0279d74b.mjs +12 -0
- package/dist/webimage.5ac7ce95.mjs +32 -0
- package/{dist → dist-tsc}/index.js +0 -0
- package/package.json +23 -21
- package/src/index.js +7 -0
- package/src/setup.js +143 -0
- package/dist/setup.js +0 -96
@@ -0,0 +1,12 @@
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import { B as BaseDecoder } from "./index.7dac8670.mjs";
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import "react";
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import "@vitessce/vit-s";
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import "react-dom";
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class RawDecoder extends BaseDecoder {
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decodeBlock(buffer) {
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return buffer;
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}
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}
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export {
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RawDecoder as default
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};
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import { B as BaseDecoder } from "./index.7dac8670.mjs";
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import "react";
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import "@vitessce/vit-s";
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import "react-dom";
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class WebImageDecoder extends BaseDecoder {
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constructor() {
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super();
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if (typeof createImageBitmap === "undefined") {
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throw new Error("Cannot decode WebImage as `createImageBitmap` is not available");
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} else if (typeof document === "undefined" && typeof OffscreenCanvas === "undefined") {
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throw new Error("Cannot decode WebImage as neither `document` nor `OffscreenCanvas` is not available");
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}
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}
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async decode(fileDirectory, buffer) {
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const blob = new Blob([buffer]);
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const imageBitmap = await createImageBitmap(blob);
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let canvas;
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if (typeof document !== "undefined") {
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canvas = document.createElement("canvas");
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canvas.width = imageBitmap.width;
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canvas.height = imageBitmap.height;
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} else {
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canvas = new OffscreenCanvas(imageBitmap.width, imageBitmap.height);
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}
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const ctx = canvas.getContext("2d");
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ctx.drawImage(imageBitmap, 0, 0);
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return ctx.getImageData(0, 0, imageBitmap.width, imageBitmap.height).data.buffer;
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}
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}
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export {
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WebImageDecoder as default
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};
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File without changes
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package/package.json
CHANGED
@@ -1,6 +1,6 @@
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{
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"name": "@vitessce/all",
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"version": "2.0.3
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"version": "2.0.3",
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"author": "Gehlenborg Lab",
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"homepage": "http://vitessce.io",
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"repository": {
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"url": "git+https://github.com/vitessce/vitessce.git"
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},
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"license": "MIT",
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"main": "dist/index.
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"main": "dist/index.mjs",
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"files": [
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"dist"
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"dist",
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"src"
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],
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"dependencies": {
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"@material-ui/core": "~4.12.3",
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"@vitessce/constants-internal": "2.0.3
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/json": "2.0.3
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"@vitessce/
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"@vitessce/
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"@vitessce/scatterplot-
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/
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"@vitessce/constants-internal": "2.0.3",
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"@vitessce/csv": "2.0.3",
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"@vitessce/description": "2.0.3",
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"@vitessce/feature-list": "2.0.3",
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"@vitessce/genomic-profiles": "2.0.3",
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"@vitessce/heatmap": "2.0.3",
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"@vitessce/json": "2.0.3",
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"@vitessce/layer-controller": "2.0.3",
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"@vitessce/obs-sets-manager": "2.0.3",
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"@vitessce/scatterplot-embedding": "2.0.3",
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"@vitessce/scatterplot-gating": "2.0.3",
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"@vitessce/spatial": "2.0.3",
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"@vitessce/statistical-plots": "2.0.3",
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"@vitessce/status": "2.0.3",
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"@vitessce/vit-s": "2.0.3",
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"@vitessce/zarr": "2.0.3"
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},
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"devDependencies": {
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"react": "^18.0.0"
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"react": "^16.8.0 || ^17.0.0 || ^18.0.0"
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},
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"scripts": {
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"start": "tsc
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"build": "tsc"
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"start": "pnpm -C ../../../ run start-tsc",
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"build": "pnpm -C ../../../ run build-tsc",
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"bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js"
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}
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}
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package/src/index.js
ADDED
package/src/setup.js
ADDED
@@ -0,0 +1,143 @@
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/* eslint-disable max-len */
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import { useState, useLayoutEffect } from 'react';
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import { VitS, registerPluginFileType } from '@vitessce/vit-s';
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// Register view type plugins
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import { register as registerDescription } from '@vitessce/description';
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import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
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import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
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import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
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import { register as registerSpatial } from '@vitessce/spatial';
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import { register as registerHeatmap } from '@vitessce/heatmap';
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import { register as registerFeatureList } from '@vitessce/feature-list';
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import { register as registerLayerController } from '@vitessce/layer-controller';
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import { register as registerStatus } from '@vitessce/status';
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import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
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import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
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// Register file type plugins
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import {
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// CSV
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CsvSource,
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ObsSetsCsvLoader,
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ObsEmbeddingCsvLoader,
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ObsLocationsCsvLoader,
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ObsLabelsCsvLoader,
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ObsFeatureMatrixCsvLoader,
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FeatureLabelsCsvLoader,
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} from '@vitessce/csv';
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import {
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// JSON
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JsonSource,
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JsonLoader,
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ObsSegmentationsJsonLoader,
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ObsSetsJsonLoader,
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// Legacy
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RasterJsonAsImageLoader,
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RasterJsonAsObsSegmentationsLoader,
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ClustersJsonAsObsFeatureMatrixLoader,
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GenesJsonAsObsFeatureMatrixLoader,
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CellsJsonAsObsLabelsLoader,
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CellsJsonAsObsEmbeddingLoader,
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CellsJsonAsObsLocationsLoader,
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CellsJsonAsObsSegmentationsLoader,
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MoleculesJsonAsObsLocationsLoader,
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MoleculesJsonAsObsLabelsLoader,
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} from '@vitessce/json';
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import {
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// AnnData
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AnnDataSource,
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ObsFeatureMatrixAnndataLoader,
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ObsEmbeddingAnndataLoader,
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ObsLocationsAnndataLoader,
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ObsSegmentationsAnndataLoader,
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ObsSetsAnndataLoader,
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ObsLabelsAnndataLoader,
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FeatureLabelsAnndataLoader,
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// MuData
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MuDataSource,
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// OME
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OmeZarrLoader,
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// Legacy
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ZarrDataSource,
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MatrixZarrAsObsFeatureMatrixLoader,
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GenomicProfilesZarrLoader,
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} from '@vitessce/zarr';
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import { FileType, DataType } from '@vitessce/constants-internal';
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function setup() {
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// View types
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registerDescription();
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registerObsSetsManager();
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registerScatterplotEmbedding();
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registerScatterplotGating();
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registerSpatial();
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registerHeatmap();
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registerFeatureList();
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registerLayerController();
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registerStatus();
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// Statistical plots
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registerCellSetExpression();
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registerCellSetSizes();
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registerExpressionHistogram();
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// Higlass
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registerHiglass();
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registerGenomicProfiles();
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// File types
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// All CSV file types
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registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
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registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
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// All JSON file types
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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// All AnnData file types
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registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
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registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
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// All MuData file types
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registerPluginFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource);
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registerPluginFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_MUDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, MuDataSource);
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registerPluginFileType(FileType.OBS_LABELS_MUDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, MuDataSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, MuDataSource);
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_MUDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, MuDataSource);
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registerPluginFileType(FileType.FEATURE_LABELS_MUDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, MuDataSource);
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// All OME file types
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registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
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// All legacy file types
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
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registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
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registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
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registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
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registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
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registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
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registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
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}
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export function Vitessce(props) {
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const [ready, setReady] = useState(false);
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useLayoutEffect(() => {
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setup();
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setReady(true);
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}, []);
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return (ready ? (
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<VitS {...props} />
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) : null);
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}
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package/dist/setup.js
DELETED
@@ -1,96 +0,0 @@
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import { jsx as _jsx } from "react/jsx-runtime";
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/* eslint-disable max-len */
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import { useState, useLayoutEffect } from 'react';
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import { VitS, registerPluginFileType } from '@vitessce/vit-s';
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// Register view type plugins
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import { register as registerDescription } from '@vitessce/description';
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import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
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import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
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import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
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import { register as registerSpatial } from '@vitessce/spatial';
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import { register as registerHeatmap } from '@vitessce/heatmap';
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import { register as registerFeatureList } from '@vitessce/feature-list';
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import { register as registerLayerController } from '@vitessce/layer-controller';
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import { register as registerStatus } from '@vitessce/status';
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import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
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import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
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// Register file type plugins
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import {
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// CSV
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CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
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import {
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// JSON
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JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader,
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// Legacy
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RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
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import {
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// AnnData
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AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader,
|
29
|
-
// OME
|
30
|
-
OmeZarrLoader,
|
31
|
-
// Legacy
|
32
|
-
ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
|
33
|
-
import { FileType, DataType } from '@vitessce/constants-internal';
|
34
|
-
function setup() {
|
35
|
-
// View types
|
36
|
-
registerDescription();
|
37
|
-
registerObsSetsManager();
|
38
|
-
registerScatterplotEmbedding();
|
39
|
-
registerScatterplotGating();
|
40
|
-
registerSpatial();
|
41
|
-
registerHeatmap();
|
42
|
-
registerFeatureList();
|
43
|
-
registerLayerController();
|
44
|
-
registerStatus();
|
45
|
-
// Statistical plots
|
46
|
-
registerCellSetExpression();
|
47
|
-
registerCellSetSizes();
|
48
|
-
registerExpressionHistogram();
|
49
|
-
// Higlass
|
50
|
-
registerHiglass();
|
51
|
-
registerGenomicProfiles();
|
52
|
-
// File types
|
53
|
-
// All CSV file types
|
54
|
-
registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
|
55
|
-
registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
|
56
|
-
registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
|
57
|
-
registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
|
58
|
-
registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
|
59
|
-
registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
|
60
|
-
// All JSON file types
|
61
|
-
registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
|
62
|
-
registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
|
63
|
-
// All AnnData file types
|
64
|
-
registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
|
65
|
-
registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
|
66
|
-
registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
|
67
|
-
registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
|
68
|
-
registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
|
69
|
-
registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
|
70
|
-
registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
|
71
|
-
// All OME file types
|
72
|
-
registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
|
73
|
-
// All legacy file types
|
74
|
-
registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
|
75
|
-
registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
|
76
|
-
registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
|
77
|
-
registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
|
78
|
-
registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
|
79
|
-
registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
|
80
|
-
registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
|
81
|
-
registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
|
82
|
-
registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
|
83
|
-
registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
|
84
|
-
registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
|
85
|
-
registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
|
86
|
-
registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
|
87
|
-
registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
|
88
|
-
}
|
89
|
-
export function Vitessce(props) {
|
90
|
-
const [ready, setReady] = useState(false);
|
91
|
-
useLayoutEffect(() => {
|
92
|
-
setup();
|
93
|
-
setReady(true);
|
94
|
-
}, []);
|
95
|
-
return (ready ? (_jsx(VitS, { ...props })) : null);
|
96
|
-
}
|