Coordination Types

Overview#

Vitessce defines several coordination types upon which views can be coordinated via the view config. The coordination types found on this page are all valid values for the keys of the coordinationSpace object in the view config.

dataset#

Used by the description, status, genes, cellSets, scatterplot, spatial, heatmap, layerController, cellSetSizes, genomicProfiles, cellSetExpression, and expressionHistogram components. 

embeddingType#

Used by the scatterplot component. 

embeddingZoom#

Used by the scatterplot component. Try a demo!

embeddingRotation#

Used by the scatterplot component. 

embeddingTargetX#

Used by the scatterplot component. Try a demo!

embeddingTargetY#

Used by the scatterplot component. Try a demo!

embeddingTargetZ#

Used by the scatterplot component. 

embeddingCellSetPolygonsVisible#

Used by the scatterplot component. Try a demo!

embeddingCellSetLabelsVisible#

Used by the scatterplot component. 

embeddingCellSetLabelSize#

Used by the scatterplot component. 

embeddingCellRadius#

Used by the scatterplot component. 

spatialZoom#

Used by the spatial component. 

spatialRotation#

Used by the spatial component. 

spatialTargetX#

Used by the spatial component. 

spatialTargetY#

Used by the spatial component. 

spatialTargetZ#

Used by the spatial component. 

heatmapZoomX#

Used by the heatmap component. 

heatmapZoomY#

Used by the heatmap component. 

heatmapTargetX#

Used by the heatmap component. 

heatmapTargetY#

Used by the heatmap component. 

cellFilter#

Used by the scatterplot, spatial, and heatmap components. 

cellHighlight#

Used by the status, scatterplot, spatial, and heatmap components. 

cellSetSelection#

Used by the genes, cellSets, scatterplot, spatial, heatmap, cellSetSizes, genomicProfiles, and cellSetExpression components. 

cellSetHighlight#

Used by the status, cellSets, scatterplot, spatial, heatmap, cellSetSizes, genomicProfiles, and cellSetExpression components. 

cellSetColor#

Used by the cellSets, scatterplot, spatial, heatmap, cellSetSizes, genomicProfiles, and cellSetExpression components. 

geneFilter#

Used by the genes, heatmap, and genomicProfiles components. 

geneHighlight#

Used by the status, genes, scatterplot, spatial, heatmap, and genomicProfiles components. 

geneSelection#

Used by the genes, cellSets, scatterplot, spatial, heatmap, genomicProfiles, cellSetExpression, and expressionHistogram components. 

geneExpressionColormap#

Used by the scatterplot, spatial, and heatmap components. 

geneExpressionColormapRange#

Used by the scatterplot, spatial, and heatmap components. 

cellColorEncoding#

Used by the genes, cellSets, scatterplot, spatial, and heatmap components. 

spatialLayers#

Used by the description, spatial, and layerController components. 

genomicZoomX#

Used by the genomicProfiles component. 

genomicZoomY#

Used by the genomicProfiles component. 

genomicTargetX#

Used by the genomicProfiles component. 

genomicTargetY#

Used by the genomicProfiles component. 

additionalCellSets#

Used by the cellSets, scatterplot, spatial, heatmap, cellSetSizes, genomicProfiles, and cellSetExpression components. 

moleculeHighlight#

Used by the status and spatial components. 

Constants#

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';
KeyValue
ct.DATASETdataset
ct.EMBEDDING_TYPEembeddingType
ct.EMBEDDING_ZOOMembeddingZoom
ct.EMBEDDING_ROTATIONembeddingRotation
ct.EMBEDDING_TARGET_XembeddingTargetX
ct.EMBEDDING_TARGET_YembeddingTargetY
ct.EMBEDDING_TARGET_ZembeddingTargetZ
ct.EMBEDDING_CELL_SET_POLYGONS_VISIBLEembeddingCellSetPolygonsVisible
ct.EMBEDDING_CELL_SET_LABELS_VISIBLEembeddingCellSetLabelsVisible
ct.EMBEDDING_CELL_SET_LABEL_SIZEembeddingCellSetLabelSize
ct.EMBEDDING_CELL_RADIUSembeddingCellRadius
ct.SPATIAL_ZOOMspatialZoom
ct.SPATIAL_ROTATIONspatialRotation
ct.SPATIAL_TARGET_XspatialTargetX
ct.SPATIAL_TARGET_YspatialTargetY
ct.SPATIAL_TARGET_ZspatialTargetZ
ct.HEATMAP_ZOOM_XheatmapZoomX
ct.HEATMAP_ZOOM_YheatmapZoomY
ct.HEATMAP_TARGET_XheatmapTargetX
ct.HEATMAP_TARGET_YheatmapTargetY
ct.CELL_FILTERcellFilter
ct.CELL_HIGHLIGHTcellHighlight
ct.CELL_SET_SELECTIONcellSetSelection
ct.CELL_SET_HIGHLIGHTcellSetHighlight
ct.CELL_SET_COLORcellSetColor
ct.GENE_FILTERgeneFilter
ct.GENE_HIGHLIGHTgeneHighlight
ct.GENE_SELECTIONgeneSelection
ct.GENE_EXPRESSION_COLORMAPgeneExpressionColormap
ct.GENE_EXPRESSION_COLORMAP_RANGEgeneExpressionColormapRange
ct.CELL_COLOR_ENCODINGcellColorEncoding
ct.SPATIAL_LAYERSspatialLayers
ct.GENOMIC_ZOOM_XgenomicZoomX
ct.GENOMIC_ZOOM_YgenomicZoomY
ct.GENOMIC_TARGET_XgenomicTargetX
ct.GENOMIC_TARGET_YgenomicTargetY
ct.ADDITIONAL_CELL_SETSadditionalCellSets
ct.MOLECULE_HIGHLIGHTmoleculeHighlight

Initial coordination values#

Coordination values may be defined in the coordinationSpace object in the view config upon the initial load of Vitessce. However, certain coordination values may be partially or fully dependent on data (and therefore cannot be fully specified ahead of data loading). For example, you may know ahead of time that you are most interested in certain image channels, and you would like the remaining image channel coordination values such as colors and slider domains to be automatically inferred from the image file itself. In this case, the raster loader class would need to take the initial image channels of interest as an option in the options property of the file definition, so that it can merge those initial values with the data-dependent color and slider values before updating the coordination space.

In general, there are three ways that initial coordination values may be defined:

  • in the coordinationSpace object, when the entire value is known ahead of time.
  • in the options property of a file definition (and in the file itself), when the value is partially data dependent.
  • in a file, when the value is entirely data dependent.