Constants for JS API

When writing view configs in JavaScript, it can be helpful to use the constant variables exported from the vitessce package (rather than using strings). Using constants enables type checking and autocomplete, which can prevent bugs.

View Types

We provide the ViewType constant mapping from JavaScript object keys to view type strings. For convenience, you may specify a shorter alias such as vt when the variable is imported.

import { ViewType as vt } from 'vitessce';

Key	Value
vt.DESCRIPTION	description
vt.STATUS	status
vt.SCATTERPLOT	scatterplot
vt.SPATIAL	spatial
vt.HEATMAP	heatmap
vt.LAYER_CONTROLLER	layerController
vt.GENOMIC_PROFILES	genomicProfiles
vt.GATING	gating
vt.FEATURE_LIST	featureList
vt.OBS_SETS	obsSets
vt.OBS_SET_SIZES	obsSetSizes
vt.OBS_SET_FEATURE_VALUE_DISTRIBUTION	obsSetFeatureValueDistribution
vt.FEATURE_VALUE_HISTOGRAM	featureValueHistogram

Example

import { VitessceConfig, ViewType as vt } from 'vitessce';

const vc = new VitessceConfig({ schemaVersion: "1.0.15", name: "My config" });
const dataset = vc.addDataset("My dataset");
const v1 = vc.addView(dataset, vt.SPATIAL);

Data Types

We provide the DataType and FileType constants mapping from JavaScript object keys to strings. For convenience, you may specify a shorter alias such as dt or ft when the variables are imported.

import { DataType as dt } from 'vitessce';

Key	Value
dt.OBS_LABELS	obsLabels
dt.OBS_EMBEDDING	obsEmbedding
dt.OBS_LOCATIONS	obsLocations
dt.OBS_FEATURE_MATRIX	obsFeatureMatrix
dt.OBS_SETS	obsSets
dt.FEATURE_LABELS	featureLabels
dt.IMAGE	image
dt.OBS_SEGMENTATIONS	obsSegmentations
dt.NEIGHBORHOODS	neighborhoods
dt.GENOMIC_PROFILES	genomic-profiles

File Types

import { FileType as ft } from 'vitessce';

Key	Value
ft.ANNDATA_ZARR	anndata.zarr
ft.OBS_EMBEDDING_CSV	obsEmbedding.csv
ft.OBS_LOCATIONS_CSV	obsLocations.csv
ft.OBS_LABELS_CSV	obsLabels.csv
ft.FEATURE_LABELS_CSV	featureLabels.csv
ft.OBS_FEATURE_MATRIX_CSV	obsFeatureMatrix.csv
ft.OBS_SEGMENTATIONS_JSON	obsSegmentations.json
ft.OBS_SETS_CSV	obsSets.csv
ft.OBS_SETS_JSON	obsSets.json
ft.IMAGE_OME_ZARR	image.ome-zarr
ft.OBS_FEATURE_MATRIX_ANNDATA_ZARR	obsFeatureMatrix.anndata.zarr
ft.OBS_SETS_ANNDATA_ZARR	obsSets.anndata.zarr
ft.OBS_EMBEDDING_ANNDATA_ZARR	obsEmbedding.anndata.zarr
ft.OBS_LOCATIONS_ANNDATA_ZARR	obsLocations.anndata.zarr
ft.OBS_SEGMENTATIONS_ANNDATA_ZARR	obsSegmentations.anndata.zarr
ft.OBS_LABELS_ANNDATA_ZARR	obsLabels.anndata.zarr
ft.FEATURE_LABELS_ANNDATA_ZARR	featureLabels.anndata.zarr
ft.OBS_FEATURE_MATRIX_MUDATA_ZARR	obsFeatureMatrix.mudata.zarr
ft.OBS_SETS_MUDATA_ZARR	obsSets.mudata.zarr
ft.OBS_EMBEDDING_MUDATA_ZARR	obsEmbedding.mudata.zarr
ft.OBS_LOCATIONS_MUDATA_ZARR	obsLocations.mudata.zarr
ft.OBS_SEGMENTATIONS_MUDATA_ZARR	obsSegmentations.mudata.zarr
ft.OBS_LABELS_MUDATA_ZARR	obsLabels.mudata.zarr
ft.FEATURE_LABELS_MUDATA_ZARR	featureLabels.mudata.zarr
ft.GENOMIC_PROFILES_ZARR	genomic-profiles.zarr
ft.NEIGHBORHOODS_JSON	neighborhoods.json
ft.OBS_EMBEDDING_CELLS_JSON	obsEmbedding.cells.json
ft.OBS_SEGMENTATIONS_CELLS_JSON	obsSegmentations.cells.json
ft.OBS_LOCATIONS_CELLS_JSON	obsLocations.cells.json
ft.OBS_LABELS_CELLS_JSON	obsLabels.cells.json
ft.OBS_SETS_CELL_SETS_JSON	obsSets.cell-sets.json
ft.OBS_FEATURE_MATRIX_GENES_JSON	obsFeatureMatrix.genes.json
ft.OBS_FEATURE_MATRIX_CLUSTERS_JSON	obsFeatureMatrix.clusters.json
ft.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR	obsFeatureMatrix.expression-matrix.zarr
ft.IMAGE_RASTER_JSON	image.raster.json
ft.OBS_SEGMENTATIONS_RASTER_JSON	obsSegmentations.raster.json
ft.OBS_LOCATIONS_MOLECULES_JSON	obsLocations.molecules.json
ft.OBS_LABELS_MOLECULES_JSON	obsLabels.molecules.json
ft.CELLS_JSON	cells.json
ft.CELL_SETS_JSON	cell-sets.json
ft.ANNDATA_CELL_SETS_ZARR	anndata-cell-sets.zarr
ft.ANNDATA_CELLS_ZARR	anndata-cells.zarr
ft.EXPRESSION_MATRIX_ZARR	expression-matrix.zarr
ft.MOLECULES_JSON	molecules.json
ft.RASTER_JSON	raster.json
ft.RASTER_OME_ZARR	raster.ome-zarr
ft.CLUSTERS_JSON	clusters.json
ft.GENES_JSON	genes.json
ft.ANNDATA_EXPRESSION_MATRIX_ZARR	anndata-expression-matrix.zarr

Example

import { VitessceConfig, DataType as dt, FileType as ft } from 'vitessce';

const vc = new VitessceConfig({ schemaVersion: "1.0.15", name: "My config" });
const dataset = vc.addDataset("My dataset")
    .addFile({
        url: "http://example.com/my-cell-coordinates.csv",
        fileType: ft.OBS_LOCATIONS_CSV,
        coordinationValues: { obsType: 'cell' },
    });

Coordination Types

We provide the CoordinationType constant mapping from JavaScript object keys to coordination type strings. For convenience, you may specify a shorter alias such as ct when the variable is imported.

import { CoordinationType as ct } from 'vitessce';

Key	Value
ct.DATASET	dataset
ct.OBS_TYPE	obsType
ct.FEATURE_TYPE	featureType
ct.FEATURE_VALUE_TYPE	featureValueType
ct.OBS_LABELS_TYPE	obsLabelsType
ct.EMBEDDING_TYPE	embeddingType
ct.EMBEDDING_ZOOM	embeddingZoom
ct.EMBEDDING_ROTATION	embeddingRotation
ct.EMBEDDING_TARGET_X	embeddingTargetX
ct.EMBEDDING_TARGET_Y	embeddingTargetY
ct.EMBEDDING_TARGET_Z	embeddingTargetZ
ct.EMBEDDING_OBS_SET_POLYGONS_VISIBLE	embeddingObsSetPolygonsVisible
ct.EMBEDDING_OBS_SET_LABELS_VISIBLE	embeddingObsSetLabelsVisible
ct.EMBEDDING_OBS_SET_LABEL_SIZE	embeddingObsSetLabelSize
ct.EMBEDDING_OBS_RADIUS	embeddingObsRadius
ct.EMBEDDING_OBS_RADIUS_MODE	embeddingObsRadiusMode
ct.EMBEDDING_OBS_OPACITY	embeddingObsOpacity
ct.EMBEDDING_OBS_OPACITY_MODE	embeddingObsOpacityMode
ct.SPATIAL_ZOOM	spatialZoom
ct.SPATIAL_ROTATION	spatialRotation
ct.SPATIAL_TARGET_X	spatialTargetX
ct.SPATIAL_TARGET_Y	spatialTargetY
ct.SPATIAL_TARGET_Z	spatialTargetZ
ct.SPATIAL_ROTATION_X	spatialRotationX
ct.SPATIAL_ROTATION_Y	spatialRotationY
ct.SPATIAL_ROTATION_Z	spatialRotationZ
ct.SPATIAL_ROTATION_ORBIT	spatialRotationOrbit
ct.SPATIAL_ORBIT_AXIS	spatialOrbitAxis
ct.SPATIAL_AXIS_FIXED	spatialAxisFixed
ct.HEATMAP_ZOOM_X	heatmapZoomX
ct.HEATMAP_ZOOM_Y	heatmapZoomY
ct.HEATMAP_TARGET_X	heatmapTargetX
ct.HEATMAP_TARGET_Y	heatmapTargetY
ct.OBS_FILTER	obsFilter
ct.OBS_HIGHLIGHT	obsHighlight
ct.OBS_SET_SELECTION	obsSetSelection
ct.OBS_SET_HIGHLIGHT	obsSetHighlight
ct.OBS_SET_COLOR	obsSetColor
ct.FEATURE_FILTER	featureFilter
ct.FEATURE_HIGHLIGHT	featureHighlight
ct.FEATURE_SELECTION	featureSelection
ct.FEATURE_VALUE_COLORMAP	featureValueColormap
ct.FEATURE_VALUE_TRANSFORM	featureValueTransform
ct.FEATURE_VALUE_COLORMAP_RANGE	featureValueColormapRange
ct.OBS_COLOR_ENCODING	obsColorEncoding
ct.SPATIAL_IMAGE_LAYER	spatialImageLayer
ct.SPATIAL_SEGMENTATION_LAYER	spatialSegmentationLayer
ct.SPATIAL_POINT_LAYER	spatialPointLayer
ct.SPATIAL_NEIGHBORHOOD_LAYER	spatialNeighborhoodLayer
ct.GENOMIC_ZOOM_X	genomicZoomX
ct.GENOMIC_ZOOM_Y	genomicZoomY
ct.GENOMIC_TARGET_X	genomicTargetX
ct.GENOMIC_TARGET_Y	genomicTargetY
ct.ADDITIONAL_OBS_SETS	additionalObsSets
ct.MOLECULE_HIGHLIGHT	moleculeHighlight
ct.GATING_FEATURE_SELECTION_X	gatingFeatureSelectionX
ct.GATING_FEATURE_SELECTION_Y	gatingFeatureSelectionY
ct.FEATURE_VALUE_TRANSFORM_COEFFICIENT	featureValueTransformCoefficient

Example

import { VitessceConfig, ViewType as vt, CoordinationType as ct } from 'vitessce';

const vc = new VitessceConfig({ schemaVersion: "1.0.15", name: "My config" });
const dataset = vc.addDataset("My dataset");
const v1 = vc.addView(dataset, vt.SPATIAL);
const v2 = vc.addView(dataset, vt.SPATIAL);
vc.linkViews(
    [v1, v2],
    [ct.SPATIAL_ZOOM, ct.SPATIAL_TARGET_X, ct.SPATIAL_TARGET_Y],
    [2, 0, 0]
);