Package index

All functions

SpatialExperiment-assays molecules molecules<- molecules,SpatialExperiment-method molecules<-,SpatialExperiment-method

Methods for named assays

SpatialExperiment-coercion coerce, SingleCellExperiment, SpatialExperiment-method toSpatialExperiment

SpatialExperiment coercion methods

SpatialExperiment-colData colData colData<- colData<-,SpatialExperiment,DataFrame-method colData<-,SpatialExperiment,NULL-method

SpatialExperiment colData

cbind(<SpatialExperiment>)

Combining SpatialExperiment objects

SpatialExperiment-methods spatialData spatialData<- spatialDataNames spatialDataNames<- spatialCoords spatialCoords<- spatialCoordsNames spatialCoordsNames<- imgData imgData<- scaleFactors spatialData,SpatialExperiment-method spatialData<-,SpatialExperiment,DFrame-method spatialData<-,SpatialExperiment,NULL-method spatialDataNames,SpatialExperiment-method spatialDataNames<-,SpatialExperiment,character-method spatialDataNames<-,SpatialExperiment,NULL-method spatialCoords,SpatialExperiment-method spatialCoords<-,SpatialExperiment,matrix-method spatialCoords<-,SpatialExperiment,NULL-method spatialCoordsNames,SpatialExperiment-method spatialCoordsNames<-,SpatialExperiment,character-method spatialCoordsNames<-,SpatialExperiment,NULL-method scaleFactors,SpatialExperiment-method $,SpatialExperiment-method imgData,SpatialExperiment-method imgData<-,SpatialExperiment,DataFrame-method imgData<-,SpatialExperiment,NULL-method

Methods for spatial attributes

show(<SpatialExperiment>)

Miscellaneous SpatialExperiment methods

rotateCoords(<SpatialExperiment>) mirrorCoords(<SpatialExperiment>) rotateObject(<SpatialExperiment>) mirrorObject(<SpatialExperiment>)

Methods for spatial attributes

SpatialExperiment-subset [,SpatialExperiment,ANY,ANY,ANY-method

Subsetting SpatialExperiment objects

SpatialExperiment-class SpatialExperiment

The SpatialExperiment class

SpatialImage-class SpatialImage VirtualSpatialImage-class LoadedSpatialImage-class StoredSpatialImage-class RemoteSpatialImage-class dim,VirtualSpatialImage-method dim,StoredSpatialImage-method imgRaster imgRaster,LoadedSpatialImage-method imgRaster,StoredSpatialImage-method imgRaster,RemoteSpatialImage-method imgRaster<- imgRaster<-,LoadedSpatialImage-method imgSource imgSource,LoadedSpatialImage-method imgSource,StoredSpatialImage-method imgSource,RemoteSpatialImage-method imgSource<- imgSource<-,StoredSpatialImage,character-method imgSource<-,RemoteSpatialImage,character-method coerce,VirtualSpatialImage,LoadedSpatialImage-method coerce,RemoteSpatialImage,StoredSpatialImage-method rotateImg rotateImg,VirtualSpatialImage-method rotateImg,LoadedSpatialImage-method mirrorImg mirrorImg,VirtualSpatialImage-method mirrorImg,LoadedSpatialImage-method

The SpatialImage class

show(<VirtualSpatialImage>)

Miscellaneous SpatialImage methods

getImg(<SpatialExperiment>) addImg(<SpatialExperiment>) rmvImg(<SpatialExperiment>) imgSource(<SpatialExperiment>) imgRaster(<SpatialExperiment>) rotateImg(<SpatialExperiment>) mirrorImg(<SpatialExperiment>)

Methods for handling image-related data

read10xVisium()

Load data from a 10x Genomics Visium experiment

readImgData()

Read images & scale factors for 10x Genomics Visium