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vitessce

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Vitessce app and React component library

vitessce.io

vitessce/vitessce

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import { CoordinationType, Component } from '../constants'; /** * Coordination types may have default values, * which can be defined here, and used by the * auto initialization strategy. */ export const DEFAULT_COORDINATION_VALUES = { [CoordinationType.OBS_TYPE]: 'cell', [CoordinationType.FEATURE_TYPE]: 'gene', [CoordinationType.FEATURE_VALUE_TYPE]: 'expression', [CoordinationType.EMBEDDING_ZOOM]: null, [CoordinationType.EMBEDDING_ROTATION]: 0, [CoordinationType.EMBEDDING_TARGET_X]: null, [CoordinationType.EMBEDDING_TARGET_Y]: null, [CoordinationType.EMBEDDING_TARGET_Z]: 0, [CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE]: false, [CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE]: false, [CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE]: 14, [CoordinationType.EMBEDDING_OBS_RADIUS]: 1, [CoordinationType.EMBEDDING_OBS_RADIUS_MODE]: 'auto', [CoordinationType.EMBEDDING_OBS_OPACITY]: 1, [CoordinationType.EMBEDDING_OBS_OPACITY_MODE]: 'auto', [CoordinationType.SPATIAL_ZOOM]: null, [CoordinationType.SPATIAL_ROTATION]: 0, [CoordinationType.SPATIAL_TARGET_X]: null, [CoordinationType.SPATIAL_TARGET_Y]: null, [CoordinationType.SPATIAL_TARGET_Z]: null, [CoordinationType.SPATIAL_ROTATION_X]: null, [CoordinationType.SPATIAL_ROTATION_Y]: null, [CoordinationType.SPATIAL_ROTATION_Z]: null, [CoordinationType.SPATIAL_AXIS_FIXED]: false, [CoordinationType.SPATIAL_ROTATION_ORBIT]: 0, [CoordinationType.SPATIAL_ORBIT_AXIS]: 'Y', [CoordinationType.SPATIAL_IMAGE_LAYER]: null, [CoordinationType.SPATIAL_SEGMENTATION_LAYER]: null, [CoordinationType.SPATIAL_POINT_LAYER]: null, [CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER]: null, [CoordinationType.HEATMAP_ZOOM_X]: 0, [CoordinationType.HEATMAP_ZOOM_Y]: 0, [CoordinationType.HEATMAP_TARGET_X]: 0, [CoordinationType.HEATMAP_TARGET_Y]: 0, [CoordinationType.FEATURE_VALUE_COLORMAP]: 'plasma', [CoordinationType.FEATURE_VALUE_COLORMAP_RANGE]: [0.0, 1.0], [CoordinationType.FEATURE_VALUE_TRANSFORM]: null, [CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT]: 1, [CoordinationType.FEATURE_FILTER]: null, [CoordinationType.FEATURE_HIGHLIGHT]: null, [CoordinationType.FEATURE_SELECTION]: null, [CoordinationType.OBS_FILTER]: null, [CoordinationType.OBS_HIGHLIGHT]: null, [CoordinationType.OBS_SET_SELECTION]: null, [CoordinationType.OBS_SET_HIGHLIGHT]: null, [CoordinationType.OBS_SET_COLOR]: null, [CoordinationType.OBS_COLOR_ENCODING]: 'cellSetSelection', [CoordinationType.GENOMIC_ZOOM_X]: 0, [CoordinationType.GENOMIC_ZOOM_Y]: 0, [CoordinationType.GENOMIC_TARGET_X]: 1549999999.5, [CoordinationType.GENOMIC_TARGET_Y]: 1549999999.5, [CoordinationType.ADDITIONAL_OBS_SETS]: null, [CoordinationType.MOLECULE_HIGHLIGHT]: null, [CoordinationType.GATING_FEATURE_SELECTION_X]: null, [CoordinationType.GATING_FEATURE_SELECTION_Y]: 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 = [ CoordinationType.HEATMAP_ZOOM_X, CoordinationType.HEATMAP_ZOOM_Y, CoordinationType.HEATMAP_TARGET_X, CoordinationType.HEATMAP_TARGET_Y, CoordinationType.EMBEDDING_ZOOM, CoordinationType.EMBEDDING_TARGET_X, CoordinationType.EMBEDDING_TARGET_Y, CoordinationType.EMBEDDING_TARGET_Z, CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE, CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE, CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE, CoordinationType.EMBEDDING_OBS_RADIUS, CoordinationType.EMBEDDING_OBS_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 = { [Component.SCATTERPLOT]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.EMBEDDING_TYPE, CoordinationType.EMBEDDING_ZOOM, CoordinationType.EMBEDDING_ROTATION, CoordinationType.EMBEDDING_TARGET_X, CoordinationType.EMBEDDING_TARGET_Y, CoordinationType.EMBEDDING_TARGET_Z, CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE, CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE, CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE, CoordinationType.EMBEDDING_OBS_RADIUS, CoordinationType.EMBEDDING_OBS_RADIUS_MODE, CoordinationType.EMBEDDING_OBS_OPACITY, CoordinationType.EMBEDDING_OBS_OPACITY_MODE, CoordinationType.OBS_FILTER, CoordinationType.OBS_HIGHLIGHT, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, CoordinationType.FEATURE_VALUE_COLORMAP, CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, CoordinationType.OBS_COLOR_ENCODING, CoordinationType.ADDITIONAL_OBS_SETS, ], [Component.GATING]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.EMBEDDING_TYPE, CoordinationType.EMBEDDING_ZOOM, CoordinationType.EMBEDDING_ROTATION, CoordinationType.EMBEDDING_TARGET_X, CoordinationType.EMBEDDING_TARGET_Y, CoordinationType.EMBEDDING_TARGET_Z, CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE, CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE, CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE, CoordinationType.EMBEDDING_OBS_RADIUS, CoordinationType.EMBEDDING_OBS_RADIUS_MODE, CoordinationType.EMBEDDING_OBS_OPACITY, CoordinationType.EMBEDDING_OBS_OPACITY_MODE, CoordinationType.OBS_FILTER, CoordinationType.OBS_HIGHLIGHT, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, CoordinationType.FEATURE_VALUE_COLORMAP, CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, CoordinationType.OBS_COLOR_ENCODING, CoordinationType.ADDITIONAL_OBS_SETS, CoordinationType.FEATURE_VALUE_TRANSFORM, CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT, CoordinationType.GATING_FEATURE_SELECTION_X, CoordinationType.GATING_FEATURE_SELECTION_Y, ], [Component.SPATIAL]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.SPATIAL_ZOOM, CoordinationType.SPATIAL_ROTATION, CoordinationType.SPATIAL_IMAGE_LAYER, CoordinationType.SPATIAL_SEGMENTATION_LAYER, CoordinationType.SPATIAL_POINT_LAYER, CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER, CoordinationType.SPATIAL_TARGET_X, CoordinationType.SPATIAL_TARGET_Y, CoordinationType.SPATIAL_TARGET_Z, CoordinationType.SPATIAL_ROTATION_X, CoordinationType.SPATIAL_ROTATION_Y, CoordinationType.SPATIAL_ROTATION_Z, CoordinationType.SPATIAL_ROTATION_ORBIT, CoordinationType.SPATIAL_ORBIT_AXIS, CoordinationType.SPATIAL_AXIS_FIXED, CoordinationType.OBS_FILTER, CoordinationType.OBS_HIGHLIGHT, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, CoordinationType.FEATURE_VALUE_COLORMAP, CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, CoordinationType.OBS_COLOR_ENCODING, CoordinationType.ADDITIONAL_OBS_SETS, CoordinationType.MOLECULE_HIGHLIGHT, ], [Component.HEATMAP]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.HEATMAP_ZOOM_X, CoordinationType.HEATMAP_ZOOM_Y, CoordinationType.HEATMAP_TARGET_X, CoordinationType.HEATMAP_TARGET_Y, CoordinationType.OBS_FILTER, CoordinationType.OBS_HIGHLIGHT, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.FEATURE_FILTER, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, CoordinationType.FEATURE_VALUE_COLORMAP, CoordinationType.FEATURE_VALUE_COLORMAP_RANGE, CoordinationType.OBS_COLOR_ENCODING, CoordinationType.ADDITIONAL_OBS_SETS, ], [Component.CELL_SETS]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.OBS_COLOR_ENCODING, CoordinationType.ADDITIONAL_OBS_SETS, CoordinationType.FEATURE_SELECTION, ], [Component.CELL_SET_SIZES]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.ADDITIONAL_OBS_SETS, ], [Component.STATUS]: [ CoordinationType.DATASET, CoordinationType.OBS_HIGHLIGHT, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.MOLECULE_HIGHLIGHT, ], [Component.GENES]: [ CoordinationType.DATASET, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_FILTER, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, CoordinationType.OBS_COLOR_ENCODING, CoordinationType.OBS_SET_SELECTION, ], [Component.CELL_SET_EXPRESSION]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.FEATURE_SELECTION, CoordinationType.FEATURE_VALUE_TRANSFORM, CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.ADDITIONAL_OBS_SETS, ], [Component.EXPRESSION_HISTOGRAM]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.FEATURE_SELECTION, ], [Component.LAYER_CONTROLLER]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.SPATIAL_IMAGE_LAYER, CoordinationType.SPATIAL_SEGMENTATION_LAYER, CoordinationType.SPATIAL_POINT_LAYER, CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER, CoordinationType.SPATIAL_ZOOM, CoordinationType.SPATIAL_TARGET_X, CoordinationType.SPATIAL_TARGET_Y, CoordinationType.SPATIAL_TARGET_Z, CoordinationType.SPATIAL_ROTATION_X, CoordinationType.SPATIAL_ROTATION_Y, CoordinationType.SPATIAL_ROTATION_Z, CoordinationType.SPATIAL_ROTATION_ORBIT, CoordinationType.SPATIAL_ORBIT_AXIS, ], [Component.GENOMIC_PROFILES]: [ CoordinationType.DATASET, CoordinationType.OBS_TYPE, CoordinationType.FEATURE_TYPE, CoordinationType.FEATURE_VALUE_TYPE, CoordinationType.GENOMIC_ZOOM_X, CoordinationType.GENOMIC_ZOOM_Y, CoordinationType.GENOMIC_TARGET_X, CoordinationType.GENOMIC_TARGET_Y, CoordinationType.FEATURE_FILTER, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, CoordinationType.OBS_SET_SELECTION, CoordinationType.OBS_SET_HIGHLIGHT, CoordinationType.OBS_SET_COLOR, CoordinationType.ADDITIONAL_OBS_SETS, ], [Component.DESCRIPTION]: [ CoordinationType.DATASET, CoordinationType.SPATIAL_IMAGE_LAYER, ], higlass: [ CoordinationType.DATASET, CoordinationType.GENOMIC_ZOOM_X, CoordinationType.GENOMIC_ZOOM_Y, CoordinationType.GENOMIC_TARGET_X, CoordinationType.GENOMIC_TARGET_Y, CoordinationType.FEATURE_FILTER, CoordinationType.FEATURE_HIGHLIGHT, CoordinationType.FEATURE_SELECTION, ], };