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vitessce

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Vitessce app and React component library

vitessce.io

vitessce/vitessce

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/** * Constants representing names of coordination types, * to help prevent typos. */ export const COORDINATION_TYPES = { DATASET: 'dataset', EMBEDDING_TYPE: 'embeddingType', EMBEDDING_ZOOM: 'embeddingZoom', EMBEDDING_ROTATION: 'embeddingRotation', EMBEDDING_TARGET_X: 'embeddingTargetX', EMBEDDING_TARGET_Y: 'embeddingTargetY', EMBEDDING_TARGET_Z: 'embeddingTargetZ', EMBEDDING_CELL_SET_POLYGONS_VISIBLE: 'embeddingCellSetPolygonsVisible', EMBEDDING_CELL_SET_LABELS_VISIBLE: 'embeddingCellSetLabelsVisible', EMBEDDING_CELL_SET_LABEL_SIZE: 'embeddingCellSetLabelSize', EMBEDDING_CELL_RADIUS: 'embeddingCellRadius', EMBEDDING_CELL_OPACITY: 'embeddingCellOpacity', EMBEDDING_CELL_RADIUS_MODE: 'embeddingCellRadiusMode', EMBEDDING_CELL_OPACITY_MODE: 'embeddingCellOpacityMode', SPATIAL_ZOOM: 'spatialZoom', SPATIAL_ROTATION: 'spatialRotation', SPATIAL_TARGET_X: 'spatialTargetX', SPATIAL_TARGET_Y: 'spatialTargetY', SPATIAL_TARGET_Z: 'spatialTargetZ', SPATIAL_ROTATION_X: 'spatialRotationX', SPATIAL_ROTATION_Y: 'spatialRotationY', SPATIAL_ROTATION_Z: 'spatialRotationZ', SPATIAL_ROTATION_ORBIT: 'spatialRotationOrbit', SPATIAL_ORBIT_AXIS: 'spatialOrbitAxis', SPATIAL_AXIS_FIXED: 'spatialAxisFixed', HEATMAP_ZOOM_X: 'heatmapZoomX', HEATMAP_ZOOM_Y: 'heatmapZoomY', HEATMAP_TARGET_X: 'heatmapTargetX', HEATMAP_TARGET_Y: 'heatmapTargetY', CELL_FILTER: 'cellFilter', CELL_HIGHLIGHT: 'cellHighlight', CELL_SET_SELECTION: 'cellSetSelection', CELL_SET_HIGHLIGHT: 'cellSetHighlight', CELL_SET_COLOR: 'cellSetColor', GENE_FILTER: 'geneFilter', GENE_HIGHLIGHT: 'geneHighlight', GENE_SELECTION: 'geneSelection', GENE_EXPRESSION_COLORMAP: 'geneExpressionColormap', GENE_EXPRESSION_TRANSFORM: 'geneExpressionTransform', GENE_EXPRESSION_COLORMAP_RANGE: 'geneExpressionColormapRange', CELL_COLOR_ENCODING: 'cellColorEncoding', SPATIAL_RASTER_LAYERS: 'spatialRasterLayers', SPATIAL_CELLS_LAYER: 'spatialCellsLayer', SPATIAL_MOLECULES_LAYER: 'spatialMoleculesLayer', SPATIAL_NEIGHBORHOODS_LAYER: 'spatialNeighborhoodsLayer', GENOMIC_ZOOM_X: 'genomicZoomX', GENOMIC_ZOOM_Y: 'genomicZoomY', GENOMIC_TARGET_X: 'genomicTargetX', GENOMIC_TARGET_Y: 'genomicTargetY', ADDITIONAL_CELL_SETS: 'additionalCellSets', MOLECULE_HIGHLIGHT: 'moleculeHighlight', }; /** * Coordination types may have default values, * which can be defined here, and used by the * auto initialization strategy. */ export const DEFAULT_COORDINATION_VALUES = { [COORDINATION_TYPES.EMBEDDING_ZOOM]: null, [COORDINATION_TYPES.EMBEDDING_ROTATION]: 0, [COORDINATION_TYPES.EMBEDDING_TARGET_X]: null, [COORDINATION_TYPES.EMBEDDING_TARGET_Y]: null, [COORDINATION_TYPES.EMBEDDING_TARGET_Z]: 0, [COORDINATION_TYPES.EMBEDDING_CELL_SET_POLYGONS_VISIBLE]: false, [COORDINATION_TYPES.EMBEDDING_CELL_SET_LABELS_VISIBLE]: false, [COORDINATION_TYPES.EMBEDDING_CELL_SET_LABEL_SIZE]: 14, [COORDINATION_TYPES.EMBEDDING_CELL_RADIUS]: 1, [COORDINATION_TYPES.EMBEDDING_CELL_RADIUS_MODE]: 'auto', [COORDINATION_TYPES.EMBEDDING_CELL_OPACITY]: 1, [COORDINATION_TYPES.EMBEDDING_CELL_OPACITY_MODE]: 'auto', [COORDINATION_TYPES.SPATIAL_ZOOM]: null, [COORDINATION_TYPES.SPATIAL_ROTATION]: 0, [COORDINATION_TYPES.SPATIAL_TARGET_X]: null, [COORDINATION_TYPES.SPATIAL_TARGET_Y]: null, [COORDINATION_TYPES.SPATIAL_TARGET_Z]: null, [COORDINATION_TYPES.SPATIAL_ROTATION_X]: null, [COORDINATION_TYPES.SPATIAL_ROTATION_Y]: null, [COORDINATION_TYPES.SPATIAL_ROTATION_Z]: null, [COORDINATION_TYPES.SPATIAL_AXIS_FIXED]: false, [COORDINATION_TYPES.SPATIAL_ROTATION_ORBIT]: 0, [COORDINATION_TYPES.SPATIAL_ORBIT_AXIS]: 'Y', [COORDINATION_TYPES.SPATIAL_RASTER_LAYERS]: null, [COORDINATION_TYPES.SPATIAL_CELLS_LAYER]: null, [COORDINATION_TYPES.SPATIAL_MOLECULES_LAYER]: null, [COORDINATION_TYPES.SPATIAL_NEIGHBORHOODS_LAYER]: null, [COORDINATION_TYPES.HEATMAP_ZOOM_X]: 0, [COORDINATION_TYPES.HEATMAP_ZOOM_Y]: 0, [COORDINATION_TYPES.HEATMAP_TARGET_X]: 0, [COORDINATION_TYPES.HEATMAP_TARGET_Y]: 0, [COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP]: 'plasma', [COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP_RANGE]: [0.0, 1.0], [COORDINATION_TYPES.GENE_EXPRESSION_TRANSFORM]: null, [COORDINATION_TYPES.GENE_FILTER]: null, [COORDINATION_TYPES.GENE_HIGHLIGHT]: null, [COORDINATION_TYPES.GENE_SELECTION]: null, [COORDINATION_TYPES.CELL_FILTER]: null, [COORDINATION_TYPES.CELL_HIGHLIGHT]: null, [COORDINATION_TYPES.CELL_SET_SELECTION]: null, [COORDINATION_TYPES.CELL_SET_HIGHLIGHT]: null, [COORDINATION_TYPES.CELL_SET_COLOR]: null, [COORDINATION_TYPES.CELL_COLOR_ENCODING]: 'cellSetSelection', [COORDINATION_TYPES.GENOMIC_ZOOM_X]: 0, [COORDINATION_TYPES.GENOMIC_ZOOM_Y]: 0, [COORDINATION_TYPES.GENOMIC_TARGET_X]: 1549999999.5, [COORDINATION_TYPES.GENOMIC_TARGET_Y]: 1549999999.5, [COORDINATION_TYPES.ADDITIONAL_CELL_SETS]: null, [COORDINATION_TYPES.MOLECULE_HIGHLIGHT]: null, }; // The following coordination types should be // initialized to independent scopes when // initialized automatically. // These make the resulting view config // (after auto-initialization) behave // like "legacy" Vitessce (pre-coordination model). export const AUTO_INDEPENDENT_COORDINATION_TYPES = [ COORDINATION_TYPES.HEATMAP_ZOOM_X, COORDINATION_TYPES.HEATMAP_ZOOM_Y, COORDINATION_TYPES.HEATMAP_TARGET_X, COORDINATION_TYPES.HEATMAP_TARGET_Y, COORDINATION_TYPES.EMBEDDING_ZOOM, COORDINATION_TYPES.EMBEDDING_TARGET_X, COORDINATION_TYPES.EMBEDDING_TARGET_Y, COORDINATION_TYPES.EMBEDDING_TARGET_Z, COORDINATION_TYPES.EMBEDDING_CELL_SET_POLYGONS_VISIBLE, COORDINATION_TYPES.EMBEDDING_CELL_SET_LABELS_VISIBLE, COORDINATION_TYPES.EMBEDDING_CELL_SET_LABEL_SIZE, COORDINATION_TYPES.EMBEDDING_CELL_RADIUS, COORDINATION_TYPES.EMBEDDING_CELL_OPACITY, ]; /** * Mapping from component type to * supported coordination object types. * This mapping can be used to determine * which pieces of state that a component will * need to get/set. * Keys here are the component registry keys. */ export const COMPONENT_COORDINATION_TYPES = { scatterplot: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.EMBEDDING_TYPE, COORDINATION_TYPES.EMBEDDING_ZOOM, COORDINATION_TYPES.EMBEDDING_ROTATION, COORDINATION_TYPES.EMBEDDING_TARGET_X, COORDINATION_TYPES.EMBEDDING_TARGET_Y, COORDINATION_TYPES.EMBEDDING_TARGET_Z, COORDINATION_TYPES.EMBEDDING_CELL_SET_POLYGONS_VISIBLE, COORDINATION_TYPES.EMBEDDING_CELL_SET_LABELS_VISIBLE, COORDINATION_TYPES.EMBEDDING_CELL_SET_LABEL_SIZE, COORDINATION_TYPES.EMBEDDING_CELL_RADIUS, COORDINATION_TYPES.EMBEDDING_CELL_RADIUS_MODE, COORDINATION_TYPES.EMBEDDING_CELL_OPACITY, COORDINATION_TYPES.EMBEDDING_CELL_OPACITY_MODE, COORDINATION_TYPES.CELL_FILTER, COORDINATION_TYPES.CELL_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.GENE_SELECTION, COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP, COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP_RANGE, COORDINATION_TYPES.CELL_COLOR_ENCODING, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, ], spatial: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.SPATIAL_ZOOM, COORDINATION_TYPES.SPATIAL_ROTATION, COORDINATION_TYPES.SPATIAL_RASTER_LAYERS, COORDINATION_TYPES.SPATIAL_CELLS_LAYER, COORDINATION_TYPES.SPATIAL_MOLECULES_LAYER, COORDINATION_TYPES.SPATIAL_NEIGHBORHOODS_LAYER, COORDINATION_TYPES.SPATIAL_TARGET_X, COORDINATION_TYPES.SPATIAL_TARGET_Y, COORDINATION_TYPES.SPATIAL_TARGET_Z, COORDINATION_TYPES.SPATIAL_ROTATION_X, COORDINATION_TYPES.SPATIAL_ROTATION_Y, COORDINATION_TYPES.SPATIAL_ROTATION_Z, COORDINATION_TYPES.SPATIAL_ROTATION_ORBIT, COORDINATION_TYPES.SPATIAL_ORBIT_AXIS, COORDINATION_TYPES.SPATIAL_AXIS_FIXED, COORDINATION_TYPES.CELL_FILTER, COORDINATION_TYPES.CELL_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.GENE_SELECTION, COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP, COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP_RANGE, COORDINATION_TYPES.CELL_COLOR_ENCODING, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, COORDINATION_TYPES.MOLECULE_HIGHLIGHT, ], heatmap: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.HEATMAP_ZOOM_X, COORDINATION_TYPES.HEATMAP_ZOOM_Y, COORDINATION_TYPES.HEATMAP_TARGET_X, COORDINATION_TYPES.HEATMAP_TARGET_Y, COORDINATION_TYPES.CELL_FILTER, COORDINATION_TYPES.CELL_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.GENE_FILTER, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.GENE_SELECTION, COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP, COORDINATION_TYPES.GENE_EXPRESSION_COLORMAP_RANGE, COORDINATION_TYPES.CELL_COLOR_ENCODING, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, ], cellSets: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.CELL_COLOR_ENCODING, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, ], cellSetSizes: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, ], cellSetExpression: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.GENE_SELECTION, COORDINATION_TYPES.GENE_EXPRESSION_TRANSFORM, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, ], status: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.CELL_HIGHLIGHT, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.MOLECULE_HIGHLIGHT, ], genes: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.GENE_FILTER, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.GENE_SELECTION, COORDINATION_TYPES.CELL_COLOR_ENCODING, ], expressionHistogram: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.GENE_SELECTION, ], layerController: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.SPATIAL_RASTER_LAYERS, COORDINATION_TYPES.SPATIAL_CELLS_LAYER, COORDINATION_TYPES.SPATIAL_MOLECULES_LAYER, COORDINATION_TYPES.SPATIAL_NEIGHBORHOODS_LAYER, COORDINATION_TYPES.SPATIAL_ZOOM, COORDINATION_TYPES.SPATIAL_TARGET_X, COORDINATION_TYPES.SPATIAL_TARGET_Y, COORDINATION_TYPES.SPATIAL_TARGET_Z, COORDINATION_TYPES.SPATIAL_ROTATION_X, COORDINATION_TYPES.SPATIAL_ROTATION_Y, COORDINATION_TYPES.SPATIAL_ROTATION_Z, COORDINATION_TYPES.SPATIAL_ROTATION_ORBIT, COORDINATION_TYPES.SPATIAL_ORBIT_AXIS, ], higlass: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.GENOMIC_ZOOM_X, COORDINATION_TYPES.GENOMIC_ZOOM_Y, COORDINATION_TYPES.GENOMIC_TARGET_X, COORDINATION_TYPES.GENOMIC_TARGET_Y, COORDINATION_TYPES.GENE_FILTER, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.GENE_SELECTION, ], genomicProfiles: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.GENOMIC_ZOOM_X, COORDINATION_TYPES.GENOMIC_ZOOM_Y, COORDINATION_TYPES.GENOMIC_TARGET_X, COORDINATION_TYPES.GENOMIC_TARGET_Y, COORDINATION_TYPES.GENE_FILTER, COORDINATION_TYPES.GENE_HIGHLIGHT, COORDINATION_TYPES.GENE_SELECTION, COORDINATION_TYPES.CELL_SET_SELECTION, COORDINATION_TYPES.CELL_SET_HIGHLIGHT, COORDINATION_TYPES.CELL_SET_COLOR, COORDINATION_TYPES.ADDITIONAL_CELL_SETS, ], description: [ COORDINATION_TYPES.DATASET, COORDINATION_TYPES.SPATIAL_RASTER_LAYERS, ], };