vitessce/src/demo/view-configs/eng.js

Vitessce app and React component library

import {
  makeDatasetNameToJsonFiles,
  getS3Url, vapi,
} from '../utils';

const driesName = 'Eng et al., Nature 2019';
const driesDescription = 'Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH';

export const eng2019 = {
  name: driesName,
  version: '1.0.0',
  description: driesDescription,
  public: true,
  datasets: [
    {
      uid: 'dries-2019',
      name: 'Dries 2019',
      files: [
        'cells',
        'cell-sets',
      ].map(makeDatasetNameToJsonFiles('dries')),
    },
  ],
  initStrategy: 'auto',
  coordinationSpace: {
    embeddingType: {
      TSNE: 't-SNE',
      UMAP: 'UMAP',
    },
    embeddingCellSetPolygonsVisible: {
      A: false,
    },
    embeddingCellSetLabelsVisible: {
      A: true,
    },
    embeddingCellSetLabelSize: {
      A: 16,
    },
    embeddingCellRadius: {
      A: 1,
    },
    embeddingZoom: {
      TSNE: 3,
      UMAP: 3,
    },
    spatialZoom: {
      A: -4.4,
    },
    spatialTargetX: {
      A: 3800,
    },
    spatialTargetY: {
      A: -900,
    },
  },
  layout: [
    {
      component: 'description',
      props: {
        description: `${driesName}: ${driesDescription}`,
      },
      x: 9,
      y: 0,
      w: 3,
      h: 2,
    },
    {
      component: 'status',
      x: 9,
      y: 2,
      w: 3,
      h: 2,
    },
    {
      component: 'cellSets',
      x: 9,
      y: 4,
      w: 3,
      h: 4,
    },
    {
      component: 'cellSetSizes',
      x: 5,
      y: 4,
      w: 4,
      h: 4,
    },
    {
      component: 'scatterplot',
      coordinationScopes: {
        embeddingType: 'TSNE',
        embeddingZoom: 'TSNE',
        embeddingCellSetLabelsVisible: 'A',
        embeddingCellSetLabelSize: 'A',
        embeddingCellSetPolygonsVisible: 'A',
        embeddingCellRadius: 'A',
      },
      x: 0,
      y: 2,
      w: 5,
      h: 4,
    },
    {
      component: 'spatial',
      props: {
        cellRadius: 50,
      },
      coordinationScopes: {
        spatialZoom: 'A',
        spatialTargetX: 'A',
        spatialTargetY: 'A',
      },
      x: 5,
      y: 0,
      w: 4,
      h: 4,
    },
    {
      component: 'scatterplot',
      coordinationScopes: {
        embeddingType: 'UMAP',
        embeddingZoom: 'UMAP',
        embeddingCellSetLabelsVisible: 'A',
        embeddingCellSetLabelSize: 'A',
        embeddingCellSetPolygonsVisible: 'A',
        embeddingCellRadius: 'A',
      },
      x: 0,
      y: 0,
      w: 5,
      h: 4,
    },
  ],
};

export function getEngViewConfig(name, description) {
  const vc = new vapi.VitessceConfig('1.0.0', name, description);
  const dataset = vc.addDataset(driesName, driesDescription)
    .addFile(getS3Url('dries', 'cells'), vapi.dt.CELLS, vapi.ft.CELLS_JSON)
    .addFile(getS3Url('dries', 'cell-sets'), vapi.dt.CELL_SETS, vapi.ft.CELL_SETS_JSON);
  return [vc, dataset];
}