Package index • GiottoDB

Object creation

GiottoDB-class GiottoDB: GiottoDB Class
GiottoDB(): Create a new GiottoDB object
as_giotto(): Convert GiottoDB Object to giotto
as_giottodb(): Convert giotto Object to GiottoDB

Saving and loading

loadGiotto(): Load Giotto object
loadGiottoDB(): Load GiottoDB object with explicit connection
saveGiotto(): Save Giotto object

Connection management

dbReconnect(<GiottoDB>): Reconnect a GiottoDB object

Configuration

GiottoDB-options: GiottoDB Global Options

Expression processing

addStatistics(): Add statistics for Giotto / GiottoDB
calculateHVF(): Calculate Highly Variable Features for GiottoDB
normalizeGiotto(): Normalize Expression for GiottoDB with dbMatrix support
processData(): Count Matrix Processing for GiottoDB Objects

Dimension reduction

runPCA(): Run PCA on GiottoDB with dbMatrix::dbMatrix support

Differential expression

findMarkers_one_vs_all(): Find marker features one-vs-all with GiottoDB support

Subcellular workflow

calculateOverlap(<dbSpatial>,<dbSpatial>): Calculate overlaps with dbSpatial-backed objects
createGiottoPoints(<dbSpatial>): Create GiottoPoints object using dbSpatial
createGiottoPolygon(<dbSpatial>): Create GiottoPolygon object using dbSpatial
overlapToMatrix(<dbSpatial>): Convert dbSpatial overlaps to a matrix
tessellate(): Tessellate a dbSpatial object

Visualization

spatInSituPlotPoints(): Plot in situ points with GiottoDB support