Skip to main content

Coordination Types

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. 

embeddingCellRadiusMode 

Used by the scatterplot component. 

embeddingCellOpacity 

Used by the scatterplot component. 

embeddingCellOpacityMode 

Used by the scatterplot component. 

spatialZoom 

Used by the spatial and layerController components. 

spatialRotation 

Used by the spatial component. 

spatialTargetX 

Used by the spatial and layerController components. 

spatialTargetY 

Used by the spatial and layerController components. 

spatialTargetZ 

Used by the spatial and layerController components. 

spatialRotationX 

Used by the spatial and layerController components. 

spatialRotationY 

Used by the spatial and layerController components. 

spatialRotationZ 

Used by the spatial and layerController components. 

spatialRotationOrbit 

Used by the spatial and layerController components. 

spatialOrbitAxis 

Used by the spatial and layerController components. 

spatialAxisFixed 

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. 

geneExpressionTransform 

Used by the cellSetExpression component. 

geneExpressionColormapRange 

Used by the scatterplot, spatial, and heatmap components. 

cellColorEncoding 

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

spatialRasterLayers 

Used by the description, spatial, and layerController components. 

spatialCellsLayer 

Used by the spatial and layerController components. 

spatialMoleculesLayer 

Used by the spatial and layerController components. 

spatialNeighborhoodsLayer 

Used by the 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. 

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.