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.
embeddingZoom
Used by the scatterplot
component. Try a demo!
embeddingTargetX
Used by the scatterplot
component. Try a demo!
embeddingTargetY
Used by the scatterplot
component. Try a demo!
embeddingCellSetPolygonsVisible
Used by the scatterplot
component. Try a demo!
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.
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.
additionalCellSets
Used by the cellSets
, scatterplot
, spatial
, heatmap
, cellSetSizes
, genomicProfiles
, and cellSetExpression
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.