Package index

Read SpatialData

readImage() readLabel() readPoint() readShape() readTable() readSpatialData()

Reading `SpatialData`

Methods for SpatialData objects or their components

CTgraph(<SpatialData>) CTgraph(<SpatialDataElement>) CTgraph(<ANY>) CTpath(<SpatialData>) CTpath(<SpatialDataElement>) CTpath(<ANY>) CTplot()

Coord. trans. graph

axes(<SpatialDataAttrs>) CTlist(<SpatialDataAttrs>) CTdata(<SpatialDataAttrs>) CTtype(<SpatialDataAttrs>) CTname(<SpatialDataAttrs>) axes(<SpatialDataElement>) CTlist(<SpatialDataElement>) CTtype(<SpatialDataElement>) CTname(<SpatialDataElement>) CTdata(<SpatialDataElement>) CTname(<SpatialData>) rmvCT(<SpatialDataElement>) rmvCT(<SpatialDataAttrs>) addCT(<SpatialDataElement>) addCT(<SpatialDataAttrs>)

Coord. trans. utilities

SpatialData() `$`(<SpatialData>) `$<-`(<SpatialData>) `[[`(<SpatialData>,<numeric>,<ANY>) `[[`(<SpatialData>,<character>,<ANY>) data(<ANY>) meta(<SpatialDataElement>) `[`(<SpatialData>,<ANY>,<ANY>,<ANY>) rownames(<SpatialData>) colnames(<SpatialData>) layer(<SpatialData>,<character>) layer(<SpatialData>,<ANY>) element(<SpatialData>,<character>) element(<SpatialData>,<numeric>) element(<SpatialData>,<missing>) element(<SpatialData>,<ANY>) `element<-`(<SpatialData>,<character>) images(<SpatialData>) labels(<SpatialData>) points(<SpatialData>) shapes(<SpatialData>) tables(<SpatialData>) table(<ANY>) `[[<-`(<SpatialData>,<numeric>,<ANY>) `[[<-`(<SpatialData>,<character>,<ANY>)

The `SpatialData` class

SpatialDataImage() SpatialDataLabel() dim(<SpatialDataArray>) length(<SpatialDataArray>) data_type(<SpatialDataArray>) data_type(<DelayedArray>) channels(<SpatialDataAttrs>) channels(<SpatialDataImage>) channels(<SpatialDataElement>) `[`(<SpatialDataImage>,<ANY>,<ANY>,<ANY>) `[`(<SpatialDataLabel>,<ANY>,<ANY>,<ANY>)

SpatialDataArray

SpatialDataAttrs() `$`(<SpatialDataAttrs>) feature_key(<SpatialDataPoint>) feature_key(<SpatialDataAttrs>) `feature_key<-`(<SpatialDataAttrs>,<character>) region_key(<SingleCellExperiment>) region(<SingleCellExperiment>) regions(<SingleCellExperiment>) `regions<-`(<SingleCellExperiment>,<character>) `regions<-`(<SingleCellExperiment>,<NULL>) instance_key(<list>) instance_key(<SingleCellExperiment>) instance_key(<SpatialDataFrame>) instance_key(<SpatialDataLabel>) `instance_key<-`(<SpatialDataAttrs>,<character>) `instance_key<-`(<SingleCellExperiment>,<character>) instances(<SpatialDataLabel>) instances(<SpatialDataPoint>) instances(<SpatialDataShape>) instances(<SingleCellExperiment>) `instances<-`(<SingleCellExperiment>)

The `SpatialDataAttrs` class

SpatialDataPoint() SpatialDataShape() length(<SpatialDataFrame>) dim(<SpatialDataFrame>) names(<SpatialDataFrame>) as.data.frame(<SpatialDataFrame>) geom_type(<SpatialDataShape>) pull(<SpatialDataFrame>) select(<SpatialDataFrame>) mutate(<SpatialDataFrame>) filter(<SpatialDataFrame>) `[[`(<SpatialDataFrame>,<ANY>,<ANY>) `$`(<SpatialDataPoint>) .DollarNames(<SpatialDataShape>) `$`(<SpatialDataShape>) `[`(<SpatialDataFrame>,<ANY>,<ANY>,<ANY>)

SpatialDataFrame

centroids(<ANY>) centroids(<SpatialDataLabel>) centroids(<SpatialDataShape>) centroids(<SpatialDataPoint>)

Spatial element centroids

combine(<SpatialData>,<SpatialData>)

Combine two SpatialData objects

crop(<SpatialDataArray>) crop(<SpatialDataFrame>) crop(<SpatialData>)

spatial cropping

extent(<SpatialData>) extent(<SpatialDataArray>) extent(<SpatialDataFrame>)

Spatial element extent

mask(<SpatialData>)

Aggregate data across layers

show(<SpatialData>) show(<SpatialDataArray>) show(<SpatialDataPoint>) show(<SpatialDataShape>)

Miscellaneous `SpatialData` methods

query(<SpatialData>)

queries

meta(<SingleCellExperiment>) hasTable(<SpatialData>,<ANY>) hasTable(<SpatialData>,<character>) getTable(<SpatialData>,<ANY>) getTable(<SpatialData>,<character>) setTable(<SpatialData>,<ANY>) setTable(<SpatialData>,<character>)

SpatialData annotations

transform(<SpatialDataElement>) sequence(<SpatialDataElement>,<list>) mirror(<SpatialDataArray>) flip(<SpatialDataArray>) flop(<SpatialDataArray>) rotate(<SpatialDataArray>,<numeric>) scale(<SpatialDataArray>,<numeric>) translation(<SpatialDataArray>,<numeric>) rotate(<SpatialDataFrame>,<numeric>) scale(<SpatialDataFrame>,<numeric>) translation(<SpatialDataFrame>,<numeric>)

Transformations

Example datasets

blobs

`SpatialData` .zarr toy datasets