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.SPATIAL_BETA | spatialBeta |
vt.HEATMAP | heatmap |
vt.LAYER_CONTROLLER | layerController |
vt.LAYER_CONTROLLER_BETA | layerControllerBeta |
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_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 |
dt.OBS_SPOTS | obsSpots |
dt.OBS_POINTS | obsPoints |
dt.OBS_LOCATIONS | obsLocations |
dt.SAMPLE_SETS | sampleSets |
dt.SAMPLE_EDGES | sampleEdges |
File Types
import { FileType as ft } from 'vitessce';
| Key | Value |
|---|---|
ft.ANNDATA_ZARR | anndata.zarr |
ft.ANNDATA_ZARR_ZIP | anndata.zarr.zip |
ft.SPATIALDATA_ZARR | spatialdata.zarr |
ft.OBS_EMBEDDING_CSV | obsEmbedding.csv |
ft.OBS_SPOTS_CSV | obsSpots.csv |
ft.OBS_POINTS_CSV | obsPoints.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.SAMPLE_SETS_CSV | sampleSets.csv |
ft.IMAGE_OME_ZARR | image.ome-zarr |
ft.OBS_SEGMENTATIONS_OME_ZARR | obsSegmentations.ome-zarr |
ft.OBS_FEATURE_MATRIX_ANNDATA_ZARR | obsFeatureMatrix.anndata.zarr |
ft.OBS_FEATURE_COLUMNS_ANNDATA_ZARR | obsFeatureColumns.anndata.zarr |
ft.OBS_SETS_ANNDATA_ZARR | obsSets.anndata.zarr |
ft.OBS_EMBEDDING_ANNDATA_ZARR | obsEmbedding.anndata.zarr |
ft.OBS_SPOTS_ANNDATA_ZARR | obsSpots.anndata.zarr |
ft.OBS_POINTS_ANNDATA_ZARR | obsPoints.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.SAMPLE_EDGES_ANNDATA_ZARR | sampleEdges.anndata.zarr |
ft.OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP | obsFeatureMatrix.anndata.zarr.zip |
ft.OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP | obsFeatureColumns.anndata.zarr.zip |
ft.OBS_SETS_ANNDATA_ZARR_ZIP | obsSets.anndata.zarr.zip |
ft.OBS_EMBEDDING_ANNDATA_ZARR_ZIP | obsEmbedding.anndata.zarr.zip |
ft.OBS_SPOTS_ANNDATA_ZARR_ZIP | obsSpots.anndata.zarr.zip |
ft.OBS_POINTS_ANNDATA_ZARR_ZIP | obsPoints.anndata.zarr.zip |
ft.OBS_LOCATIONS_ANNDATA_ZARR_ZIP | obsLocations.anndata.zarr.zip |
ft.OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP | obsSegmentations.anndata.zarr.zip |
ft.OBS_LABELS_ANNDATA_ZARR_ZIP | obsLabels.anndata.zarr.zip |
ft.FEATURE_LABELS_ANNDATA_ZARR_ZIP | featureLabels.anndata.zarr.zip |
ft.SAMPLE_EDGES_ANNDATA_ZARR_ZIP | sampleEdges.anndata.zarr.zip |
ft.IMAGE_SPATIALDATA_ZARR | image.spatialdata.zarr |
ft.LABELS_SPATIALDATA_ZARR | labels.spatialdata.zarr |
ft.SHAPES_SPATIALDATA_ZARR | shapes.spatialdata.zarr |
ft.OBS_FEATURE_MATRIX_SPATIALDATA_ZARR | obsFeatureMatrix.spatialdata.zarr |
ft.OBS_SETS_SPATIALDATA_ZARR | obsSets.spatialdata.zarr |
ft.OBS_SPOTS_SPATIALDATA_ZARR | obsSpots.spatialdata.zarr |
ft.FEATURE_LABELS_SPATIALDATA_ZARR | featureLabels.spatialdata.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_SPOTS_MUDATA_ZARR | obsSpots.mudata.zarr |
ft.OBS_POINTS_MUDATA_ZARR | obsPoints.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.IMAGE_OME_TIFF | image.ome-tiff |
ft.OBS_SEGMENTATIONS_OME_TIFF | obsSegmentations.ome-tiff |
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.META_COORDINATION_SCOPES | metaCoordinationScopes |
ct.META_COORDINATION_SCOPES_BY | metaCoordinationScopesBy |
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_TARGET_T | spatialTargetT |
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_EXPANSION | obsSetExpansion |
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 |
ct.TOOLTIPS_VISIBLE | tooltipsVisible |
ct.FILE_UID | fileUid |
ct.IMAGE_LAYER | imageLayer |
ct.IMAGE_CHANNEL | imageChannel |
ct.SEGMENTATION_LAYER | segmentationLayer |
ct.SEGMENTATION_CHANNEL | segmentationChannel |
ct.SPATIAL_TARGET_C | spatialTargetC |
ct.SPATIAL_LAYER_VISIBLE | spatialLayerVisible |
ct.SPATIAL_LAYER_OPACITY | spatialLayerOpacity |
ct.SPATIAL_LAYER_COLORMAP | spatialLayerColormap |
ct.SPATIAL_LAYER_TRANSPARENT_COLOR | spatialLayerTransparentColor |
ct.SPATIAL_LAYER_MODEL_MATRIX | spatialLayerModelMatrix |
ct.SPATIAL_SEGMENTATION_FILLED | spatialSegmentationFilled |
ct.SPATIAL_SEGMENTATION_STROKE_WIDTH | spatialSegmentationStrokeWidth |
ct.SPATIAL_CHANNEL_COLOR | spatialChannelColor |
ct.SPATIAL_CHANNEL_VISIBLE | spatialChannelVisible |
ct.SPATIAL_CHANNEL_OPACITY | spatialChannelOpacity |
ct.SPATIAL_CHANNEL_WINDOW | spatialChannelWindow |
ct.PHOTOMETRIC_INTERPRETATION | photometricInterpretation |
ct.SPATIAL_RENDERING_MODE | spatialRenderingMode |
ct.VOLUMETRIC_RENDERING_ALGORITHM | volumetricRenderingAlgorithm |
ct.SPATIAL_TARGET_RESOLUTION | spatialTargetResolution |
ct.SPATIAL_SLICE_X | spatialSliceX |
ct.SPATIAL_SLICE_Y | spatialSliceY |
ct.SPATIAL_SLICE_Z | spatialSliceZ |
ct.SPOT_LAYER | spotLayer |
ct.POINT_LAYER | pointLayer |
ct.SPATIAL_SPOT_RADIUS | spatialSpotRadius |
ct.SPATIAL_SPOT_FILLED | spatialSpotFilled |
ct.SPATIAL_SPOT_STROKE_WIDTH | spatialSpotStrokeWidth |
ct.SPATIAL_LAYER_COLOR | spatialLayerColor |
ct.PIXEL_HIGHLIGHT | pixelHighlight |
ct.TOOLTIP_CROSSHAIRS_VISIBLE | tooltipCrosshairsVisible |
ct.LEGEND_VISIBLE | legendVisible |
ct.SPATIAL_CHANNEL_LABELS_VISIBLE | spatialChannelLabelsVisible |
ct.SPATIAL_CHANNEL_LABELS_ORIENTATION | spatialChannelLabelsOrientation |
ct.SPATIAL_CHANNEL_LABEL_SIZE | spatialChannelLabelSize |
ct.SAMPLE_TYPE | sampleType |
ct.SAMPLE_SET_SELECTION | sampleSetSelection |
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]
);