Package index • GiottoClass

Giotto

Create a Giotto Object

createGiottoObject() createGiottoObjectSubcellular(): Create a giotto object

Updaters

Objects version compatibility v3.0 and up

updateGiottoObject(): Update giotto object

updateGiottoPointsObject(): Update giotto points object

updateGiottoPolygonObject(): Update giotto polygon object

Ingestion

Read

Read data in and create Giotto-native objects

readCellMetadata(): Read cell metadata

readFeatMetadata(): Read feature metadata

readPolygonData(): Read list of polygons information

readFeatData(): Read feature information

readExprData(): Read expression data

readExprMatrix(): Read expression matrix

readSpatLocsData(): Read spatial location data

readSpatNetData(): Read spatial networks

readSpatEnrichData(): Read spatial enrichment

readDimReducData(): Read dimensional reduction data

readNearestNetData(): Read nearest neighbor network data

evaluate

Evaluate and format data for usage with Giotto

evaluate_input(): Evaluate raw inputs to Giotto formatting

Create

Create Giotto-native objects

createCellMetaObj(): Create S4 cellMetaObj

createDimObj(): Create S4 dimObj

createExprObj(): Create S4 exprObj

createFeatMetaObj(): Create S4 featMetaObj

createGiottoPoints(<SpatVector>) createGiottoPoints(<data.frame>): Create giotto points object

createGiottoPolygon(<character>) createGiottoPolygon(<SpatVector>) createGiottoPolygon(<SpatRaster>) createGiottoPolygon(<data.frame>) createGiottoPolygonsFromMask() createGiottoPolygonsFromDfr() createGiottoPolygonsFromGeoJSON(): Create giotto polygons object

createNearestNetObj(): Create S4 nnNetObj

createSpatEnrObj(): Create S4 spatEnrObj

createSpatLocsObj(): Create S4 spatLocsObj

createSpatNetObj(): Create S4 spatialNetworkObj

createGiottoImage(): createGiottoImage

createGiottoLargeImage(): createGiottoLargeImage

createGiottoLargeImageList(): createGiottoLargeImageList

Access

Getters

Get data from a Giotto Object

getCellMetadata(): getCellMetadata

getFeatureMetadata(): getFeatureMetadata

getPolygonInfo(): Get polygon info

getFeatureInfo(): Get feature info

getExpression(): Get expression values

getSpatialLocations(): Get spatial locations

getSpatialNetwork(): Get spatial network

getSpatialEnrichment(): Get spatial enrichment

getDimReduction(): Get dimension reduction

getMultiomics(): Get multiomics integration results

getNearestNetwork(): Get nearest neighbor network

getGiottoImage(): Get giotto image object

spatValues() svkey(): Giotto object spatial values

Setters

Set (and replace) Giotto-native data objects in a Giotto Object

setGiotto(<giotto>,<list>) setGiotto(<giotto>,<cellMetaObj>) setGiotto(<giotto>,<featMetaObj>) setGiotto(<giotto>,<exprObj>) setGiotto(<giotto>,<giottoPoints>) setGiotto(<giotto>,<giottoPolygon>) setGiotto(<giotto>,<dimObj>) setGiotto(<giotto>,<spatLocsObj>) setGiotto(<giotto>,<spatEnrObj>) setGiotto(<giotto>,<nnNetObj>) setGiotto(<giotto>,<spatialNetworkObj>) setGiotto(<giotto>,<giottoLargeImage>) setGiotto(<giotto>,<giottoImage>): Set giotto subobjects into giotto object

setCellMetadata(): Set cell metadata

setFeatureMetadata(): Set feature metadata

setPolygonInfo(): Set polygon info

setFeatureInfo(): Set feature info

setExpression(): Set expression data

setSpatialLocations(): Set spatial locations

setSpatialNetwork(): Set spatial network

setSpatialEnrichment(): Set spatial enrichment

setDimReduction(): Set dimension reduction data

setMultiomics(): Set multiomics integration results

setNearestNetwork(): Set nearest neighbor network

setGiottoImage(): Set giotto image object

Append

Add information to the Giotto Object

addCellMetadata(): Add cell metadata

addFeatMetadata(): Add feature metadata

addGiottoImage(): addGiottoImage

addGiottoImageMG(): addGiottoImageMG

addGiottoLargeImage(): addGiottoLargeImage

Gobject Contents

Print

Print Giotto object slot contents

showGiottoCellMetadata(): showGiottoCellMetadata

showGiottoFeatMetadata(): showGiottoFeatMetadata

showGiottoSpatialInfo(): showGiottoSpatialInfo

showGiottoFeatInfo(): showGiottoFeatInfo

showGiottoExpression(): showGiottoExpression

showGiottoSpatLocs(): showGiottoSpatLocs

showGiottoSpatNetworks(): showGiottoSpatNetworks

showGiottoSpatEnrichments(): showGiottoSpatEnrichments

showGiottoDimRed(): showGiottoDimRed

showGiottoNearestNetworks(): showGiottoNearestNetworks

showGiottoImageNames(): showGiottoImageNames

Return available data

Return slot contents as data.table with nested locations

list_cell_metadata(): list_cell_metadata

list_dim_reductions(): list_dim_reductions

list_expression(): list_expression

list_feat_metadata(): list_feat_metadata

list_feature_info(): list_feature_info

list_images(): list_images

list_nearest_networks(): list_nearest_networks

list_spatial_enrichments(): list_spatial_enrichments

list_spatial_grids(): list_spatial_grids

list_spatial_info(): list_spatial_info

list_spatial_locations(): list_spatial_locations

list_spatial_networks(): list_spatial_networks

Return names of available data

List slot contents as character vector. The spat_unit and/or feat_type usually must be provided.

list_cell_id_names(): List cell ID names

list_feat_id_names(): List feat ID names

list_dim_reductions_names(): list_dim_reductions_names

list_expression_names(): list_expression_names

list_feature_info_names(): list_feature_info_names

list_images_names(): list_images_names

list_nearest_networks_names(): list_nearest_networks_names

list_spatial_enrichments_names(): list_spatial_enrichments_names

list_spatial_grids_names(): list_spatial_grids_names

list_spatial_info_names(): list_spatial_info_names

list_spatial_locations_names(): list_spatial_locations_names

list_spatial_networks_names(): list_spatial_networks_names

Annotate

Giotto object metdata and annotation tools

pDataDT(): pDataDT

fDataDT(): fDataDT

annotateGiotto(): Annotate Giotto object

removeCellAnnotation(): Remove cell annotation

removeFeatAnnotation(): Remove feature annotation

annotateSpatialNetwork(): annotateSpatialNetwork

calculateMetaTable(): calculateMetaTable

calculateMetaTableCells(): calculateMetaTableCells

calculateLabelProportions(): Calculate Proportions of Labels Per Observation Group

calculateSpatCellMetadataProportions(): calculateSpatCellMetadataProportions

Instructions

Set instructions for Giotto Object behavior

createGiottoInstructions() instructions(<missing>,<missing>) instructions(<giotto>,<missing>) instructions(<giotto>,<character>) instructions(<giottoInstructions>,<character>) `instructions<-`(<giotto>,<missing>,<missing>) `instructions<-`(<giotto>,<missing>,<logical>) `instructions<-`(<giotto>,<character>,<missing>) `instructions<-`(<giotto>,<character>,<logical>) `instructions<-`(<giottoInstructions>,<character>,<ANY>): Giotto instructions

Subset

Subsetting the Giotto Object

subsetGiotto(): subsetGiotto

subsetGiottoLocs(): Subset by spatial locations

subsetGiottoLocsMulti(): deprecated

subsetGiottoLocsSubcellular(): Subset raw subcellular information by location

Join and Split

Joining and Splitting Giotto Objects

joinGiottoObjects(): Join giotto objects

splitGiotto(): Split a Giotto Object

sliceGiotto(): Slice giotto object by spat_unit and feat_type

Data Processing

Data Processing Framework

processData(): Data Processing

processParam-class processParam: Parameter Classes for Data Processing Operations

clusterData(): Data Clustering

Poly Generation

Creation of polygon shapes and arrays

hexVertices(): Generate regular hexagon vertices

rectVertices(): Generate rectangular polygon vertices

circleVertices(): Generate circle polygon vertices

makePseudoVisium(): makePseudoVisium

polyStamp(): Spatial polygons stamp

tessellate(): Tessellated grid of polygons

triGrid() orthoGrid(): Spatial grids

Interoperability

From

Convert from other frameworks to Giotto

anndataToGiotto(): Convert anndata to Giotto

gefToGiotto(): Convert gef to Giotto

seuratToGiotto(): Deprecated

seuratToGiottoV4(): Convert a Seurat V4 object to a Giotto object

seuratToGiottoV5(): Convert a Seurat V5 object to a Giotto object

spatialExperimentToGiotto(): Utility function to convert a SpatialExperiment object to a Giotto object

spatialdataToGiotto(): Convert SpatialData to Giotto

giottoMasterToSuite(): Convert a master Giotto object to suite

To

Convert Giotto Object to other frameworks

giottoToAnnData(): Convert Giotto to anndata

giottoToSeurat(): Deprecated

giottoToSeuratV4(): Convert Giotto to Seurat V4

giottoToSeuratV5(): Convert Giotto to Seurat V5

giottoToSpatialData(): Convert Giotto to SpatialData

giottoToSpatialExperiment(): Utility function to convert a Giotto object to a SpatialExperiment object.

createBentoAdata(): Create bento adata object from gobject

Aggregate

Polygon

Polygon and spatial unit aggregation and combination

aggregateStacks(): aggregateStacks

aggregateStacksExpression(): aggregateStacksExpression

aggregateStacksLocations(): aggregateStacksLocations

aggregateStacksPolygonOverlaps(): aggregateStacksPolygonOverlaps

aggregateStacksPolygons(): aggregateStacksPolygons

combineToMultiPolygon(): Combine giottoPolygon geometries

Feature

Calculate spatial features overlapped by polygons

calculateOverlap(<giotto>,<missing>) calculateOverlap(<giottoPolygon>,<giottoPoints>) calculateOverlap(<giottoPolygon>,<giottoLargeImage>) calculateOverlap(<giottoPolygon>,<giottoAffineImage>) calculateOverlap(<giottoPolygon>,<SpatRaster>) calculateOverlap(<SpatVector>,<SpatRaster>) calculateOverlap(<SpatVector>,<SpatVector>): Calculate features overlapped by polygons

calculateOverlapRaster(): calculateOverlapRaster

calculateOverlapPolygonImages(): calculateOverlapPolygonImages

calculateOverlapSerial(): calculateOverlapSerial

calculateOverlapParallel(): calculateOverlapParallel

overlaps(<giottoPolygon>): overlaps-generic

Matrix

Convert overlapped features to raw expression matrix

overlapImagesToMatrix(): overlapImagesToMatrix

overlapToMatrix(<giotto>) overlapToMatrix(<giottoPolygon>) overlapToMatrix(<SpatVector>) overlapToMatrix(<data.table>): overlapToMatrix

overlapToMatrixMultiPoly(): overlapToMatrixMultiPoly

Centroids

Centroid calculation

addSpatialCentroidLocations(): addSpatialCentroidLocations

addSpatialCentroidLocationsLayer(): addSpatialCentroidLocationsLayer

centroids(<giottoPolygon>): centroids-generic

Combine

Create combined table of metadata and other results and data

combineCellData(): combineCellData

combineFeatureData(): combineFeatureData

combineFeatureOverlapData(): combineFeatureOverlapData

combineMetadata(): combineMetadata

combineSpatialCellMetadataInfo(): combineSpatialCellMetadataInfo

Metafeatures

Metafeature creation

createMetafeats(): createMetafeats

Classes

GiottoClass defined classes

cellMetaObj-class cellMetaObj: S4 cellMetaObj

dimObj-class dimObj: S4 dimObj Class

exprObj-class exprObj: S4 exprObj

featMetaObj-class featMetaObj: S4 featMetaObj

featureNetwork-class featureNetwork: S4 giotto feature network Class

giotto-class giotto: S4 giotto Class

giottoAffineImage-class: S4 giottoAffineImage Class

giottoImage-class giottoImage: S4 giottoImage Class

giottoLargeImage-class giottoLargeImage: S4 giottoLargeImage Class

giottoPoints-class giottoPoints: S4 giotto points Class

giottoPolygon-class giottoPolygon: S4 giotto polygon Class

miscData-class: Basic class for additional miscellaneous information

nnNetObj-class nnNetObj: S4 nnNetObj

processParam-class processParam: Parameter Classes for Data Processing Operations

spatEnrObj-class: S4 spatEnrObj Class

spatLocsObj-class spatLocsObj: S4 spatLocsObj Class

spatialGridObj-class: S4 spatialGridObj Class

spatialNetworkObj-class: S4 spatialNetworkObj Class

terraVectData-class terraVectData: Basic class for terra SpatVector-based objects

Networks

Network creation and tools

createNetwork(): Create a network

edge_distances(): Calculate network edge euclidean distances

createSpatialNetwork(): Create spatial network

createSpatialDelaunayNetwork(): Create a spatial Delaunay network

createSpatialFeaturesKNNnetwork(): Create kNN spatial feature network

createSpatialKNNnetwork(): createSpatialKNNnetwork

createSpatialWeightMatrix(): Create a spatial weight matrix

spat_net_to_igraph(): Convert spatialNetworkObj to igraph

createNearestNetwork(): createNearestNetwork

addNetworkLayout(): addNetworkLayout

Spatial

Manipulation

Spatial manipulation and terra-based functions

ext(<spatLocsObj>) ext(<giottoPolygon>) ext(<giottoPoints>) ext(<spatialNetworkObj>) ext(<giottoLargeImage>) ext(<giottoImage>) ext(<giotto>) ext(<giottoAffineImage>) ext(<affine2d>) `ext<-`(<spatLocsObj>,<SpatExtent>) `ext<-`(<spatialNetworkObj>,<SpatExtent>) `ext<-`(<giottoPoints>,<SpatExtent>) `ext<-`(<giottoPolygon>,<SpatExtent>) `ext<-`(<giottoLargeImage>,<SpatExtent>) `ext<-`(<giottoAffineImage>,<SpatExtent>) `ext<-`(<ANY>,<ANY>) `ext<-`(<giottoImage>,<SpatExtent>) `ext<-`(<affine2d>,<ANY>): Get a SpatExtent

XY(<spatLocsObj>) `XY<-`(<spatLocsObj>,<matrix>) XY(<giottoPoints>) `XY<-`(<giottoPoints>,<ANY>) XY(<giottoPolygon>) `XY<-`(<giottoPolygon>,<ANY>) XY(<SpatVector>) `XY<-`(<SpatVector>,<matrix>): Spatial coordinates

flip(<giotto>) flip(<giottoPolygon>) flip(<giottoPoints>) flip(<spatLocsObj>) flip(<spatialNetworkObj>) flip(<giottoLargeImage>) flip(<SpatExtent>) flip(<giottoAffineImage>) flip(<affine2d>): Flip an object

crop(<giottoLargeImage>) crop(<giottoAffineImage>) crop(<spatLocsObj>) crop(<spatialNetworkObj>) crop(<giottoPoints>) crop(<giottoPolygon>): Crop to a spatial subset

t(<giotto>) t(<spatLocsObj>) t(<spatialNetworkObj>) t(<giottoPoints>) t(<giottoPolygon>) t(<giottoLargeImage>) t(<giottoAffineImage>) t(<affine2d>): Transpose

spin(<giotto>) spin(<giottoPolygon>) spin(<giottoPoints>) spin(<spatLocsObj>) spin(<data.frame>) spin(<giottoLargeImage>) spin(<giottoAffineImage>) spin(<affine2d>): Spin an object

spatShift(<giotto>) spatShift(<SpatExtent>) spatShift(<spatLocsObj>) spatShift(<data.frame>) spatShift(<spatialNetworkObj>) spatShift(<giottoPolygon>) spatShift(<giottoPoints>) spatShift(<giottoLargeImage>) spatShift(<giottoImage>) spatShift(<giottoAffineImage>) spatShift(<affine2d>): Spatially shift an object

rescale(<giotto>) rescale(<spatLocsObj>) rescale(<data.frame>) rescale(<giottoPolygon>) rescale(<giottoPoints>) rescale(<giottoImage>) rescale(<giottoLargeImage>) rescale(<giottoAffineImage>) rescale(<affine2d>): Rescale an object

shear(<spatLocsObj>) shear(<SpatVector>) shear(<giottoPoints>) shear(<giottoPolygon>) shear(<giottoLargeImage>) shear(<giottoAffineImage>) shear(<affine2d>): Apply a shear tranform

affine(<giotto>,<matrix>) affine(<missing>,<missing>) affine(<ANY>,<missing>) affine(<ANY>,<affine2d>) affine(<SpatVector>,<matrix>) affine(<giottoPoints>,<matrix>) affine(<giottoPolygon>,<matrix>) affine(<spatLocsObj>,<matrix>) affine(<giottoLargeImage>,<matrix>) affine(<giottoAffineImage>,<matrix>) affine(<affine2d>,<matrix>): Affine transformations

area(<giottoPolygon>) area(<SpatVector>): Get the area of individual polygons

hull(<spatLocsObj>) hull(<giottoSpatial>) minRect() minCircle() convHull(): Convex, concave, rectangular and circular hulls

buffer(<spatLocsObj>) buffer(<giottoPoints>) buffer(<giottoPolygon>): Create a buffer around vector geometries

settleGeom(<giottoPolygon>) settleGeom(<SpatVector>): Settle polygon bounds

combineGeom(<giottoPolygon>) splitGeom(<giottoPolygon>) combineGeom(<SpatVector>) splitGeom(<SpatVector>): Combine or Split Complex Geometries

relate(<giottoSpatial>,<giottoSpatial>) relate(<giotto>,<giottoSpatial>): Spatial relationships between geometries

erase(<spatialClasses>,<spatialClasses>) snap(<giottoSpatial>) symdif(<spatialClasses>,<spatialClasses>) union(<spatialClasses>,<spatialClasses>) intersect(<spatialClasses>,<spatialClasses>): Spatial binary operations

rescalePolygons(): rescalePolygons

wrap(<giottoPolygon>) wrap(<giotto>) wrap(<giottoPoints>) vect(<packedGiottoPolygon>) vect(<packedGiottoPoints>) vect(<packedGiotto>): Wrap giotto terra pointer information

Querying

Spatial querying

spatQuery() spatQueryGiottoPolygons(): Spatial Query

Object generics

Standard generics for Giotto exported classes

plot(<giottoImage>,<missing>) plot(<giottoLargeImage>,<missing>) plot(<giottoAffineImage>,<missing>) plot(<giottoPolygon>,<missing>) plot(<giottoPoints>,<missing>) plot(<spatLocsObj>,<missing>) plot(<dimObj>,<missing>) plot(<spatialNetworkObj>,<missing>) plot(<affine2d>,<missing>): Preview a Giotto spatial object

`[`(<gdtData>,<gIndex>,<gIndex>,<missing>) `[`(<gdtData>,<logical>,<missing>,<missing>) `[`(<gdtData>,<character>,<missing>,<missing>) `[`(<gdtData>,<missing>,<numeric>,<missing>) `[`(<gdtData>,<missing>,<logical>,<missing>) `[`(<coordDataDT>,<ANY>,<ANY>,<missing>) `[`(<coordDataDT>,<missing>,<ANY>,<missing>) `[`(<coordDataDT>,<missing>,<character>,<missing>) `[`(<coordDataDT>,<ANY>,<missing>,<missing>) `[`(<coordDataDT>,<missing>,<missing>,<missing>) `[`(<giottoPoints>,<gIndex>,<missing>,<missing>) `[`(<metaData>,<missing>,<ANY>,<missing>) `[`(<metaData>,<missing>,<character>,<missing>) `[`(<metaData>,<ANY>,<missing>,<missing>) `[`(<metaData>,<missing>,<missing>,<missing>) `[`(<dimObj>,<ANY>,<ANY>,<missing>) `[`(<dimObj>,<missing>,<missing>,<missing>) `[`(<exprData>,<missing>,<ANY>,<missing>) `[`(<exprData>,<ANY>,<missing>,<missing>) `[`(<exprData>,<ANY>,<ANY>,<missing>) `[`(<exprData>,<missing>,<missing>,<missing>) `[`(<spatNetData>,<missing>,<missing>,<missing>) `[`(<nnData>,<missing>,<missing>,<missing>) `[`(<enrData>,<missing>,<missing>,<missing>) `[`(<enrData>,<ANY>,<missing>,<missing>) `[`(<enrData>,<missing>,<ANY>,<missing>) `[`(<enrData>,<missing>,<character>,<missing>) `[`(<spatGridData>,<missing>,<missing>,<missing>) `[`(<giottoPoints>,<missing>,<missing>,<missing>) `[`(<giottoPoints>,<character>,<missing>,<missing>) `[`(<giottoPoints>,<missing>,<gIndex>,<missing>) `[`(<giottoPolygon>,<missing>,<missing>,<missing>) `[`(<giottoPolygon>,<gIndex>,<missing>,<missing>) `[`(<giottoPolygon>,<character>,<missing>,<missing>) `[`(<giottoPolygon>,<missing>,<gIndex>,<missing>) `[`(<terraVectData>,<gIndex>,<gIndex>,<missing>) `[`(<giottoLargeImage>,<missing>,<missing>,<missing>) `[[`(<giottoLargeImage>,<gIndex>,<missing>) `[`(<giottoImage>,<missing>,<missing>,<missing>) `[`(<affine2d>,<missing>,<missing>,<missing>) `[`(<processParam>,<missing>,<missing>,<missing>): Subset part of an object with [ or [[

`[<-`(<coordDataDT>,<missing>,<missing>,<ANY>) `[<-`(<metaData>,<missing>,<missing>,<ANY>) `[<-`(<dimObj>,<missing>,<missing>,<ANY>) `[<-`(<exprData>,<missing>,<missing>,<ANY>) `[<-`(<spatNetData>,<missing>,<missing>,<ANY>) `[<-`(<nnData>,<missing>,<missing>,<ANY>) `[<-`(<enrData>,<missing>,<missing>,<ANY>) `[<-`(<spatGridData>,<missing>,<missing>,<ANY>) `[<-`(<giottoPoints>,<missing>,<missing>,<ANY>) `[<-`(<giottoPolygon>,<missing>,<missing>,<ANY>) `[<-`(<giottoLargeImage>,<missing>,<missing>,<ANY>) `[<-`(<giottoImage>,<missing>,<missing>,<ANY>) `[<-`(<affine2d>,<missing>,<missing>,<ANY>) `[<-`(<processParam>,<missing>,<missing>,<list>): Replace part of an object with [<-

`[`(<giotto>,<gIndex>,<missing>,<missing>) `[`(<giotto>,<missing>,<gIndex>,<missing>) `[`(<giotto>,<gIndex>,<gIndex>,<missing>) `[`(<giotto>,<missing>,<missing>,<missing>) subset(<giotto>): Subset a giotto object

`[[`(<giotto>,<missing>,<missing>) `[[`(<giotto>,<character>,<missing>) `[[`(<giotto>,<missing>,<character>) `[[`(<giotto>,<character>,<character>): Subset giotto subobjects

`$`(<giotto>) `$`(<coordDataDT>) `$`(<spatEnrObj>) `$`(<dimObj>) `$`(<metaData>) `$`(<terraVectData>) `$`(<affine2d>) `$`(<processParam>): Subset part of an object with $

`$<-`(<giotto>) `$<-`(<coordDataDT>) `$<-`(<spatEnrObj>) `$<-`(<dimObj>) `$<-`(<metaData>) `$<-`(<terraVectData>) `$<-`(<processParam>): Replace part of an object with $<-

rbind2(<cellMetaObj>,<cellMetaObj>) rbind2(<featMetaObj>,<featMetaObj>) rbind2(<spatLocsObj>,<spatLocsObj>) rbind2(<giottoPolygon>,<giottoPolygon>): Combine objects by rows (Giotto-related)

colnames(<giotto>) colnames(<exprObj>) colnames(<cellMetaObj>) colnames(<featMetaObj>) colnames(<spatEnrObj>) colnames(<spatLocsObj>) colnames(<dimObj>) rownames(<giotto>) rownames(<exprObj>) rownames(<dimObj>) rownames(<metaData>): Row and column names

dimnames(<giotto>) dimnames(<exprObj>) dimnames(<dimObj>) dimnames(<spatLocsObj>) dimnames(<metaData>) dimnames(<enrData>): Dimnames of an object

nrow(<giotto>) nrow(<giottoPoints>) nrow(<giottoPolygon>) nrow(<spatLocsObj>) nrow(<exprData>) nrow(<metaData>) nrow(<spatialNetworkObj>) nrow(<enrData>) nrow(<dimObj>) ncol(<giotto>) ncol(<exprData>) ncol(<metaData>) ncol(<enrData>) ncol(<dimObj>) dim(<giotto>) dim(<spatLocsObj>) dim(<exprData>) dim(<metaData>) dim(<enrData>) dim(<giottoLargeImage>) dim(<giottoPolygon>) dim(<giottoPoints>): Dimensions of giotto objects

copy(<coordDataDT>) copy(<giottoPoints>) copy(<giottoPolygon>) copy(<giottoLargeImage>): Copy an entire object

Hierarchical

Hierarchical tagging generics for Giotto exported classes

activeFeatType(<giotto>) `activeFeatType<-`(<giotto>,<character>): Active feature type

activeSpatUnit(<giotto>) `activeSpatUnit<-`(<giotto>,<character>): Active spatial unit

spatUnit(<ANY>) spatUnit(<giotto>) spatUnit(<list>) spatUnit(<spatData>) spatUnit(<giottoPolygon>) `spatUnit<-`(<ANY>) `spatUnit<-`(<spatData>) `spatUnit<-`(<giottoPolygon>) `spatUnit<-`(<list>) `spatUnit<-`(<giotto>) featType(<ANY>) featType(<giotto>) featType(<list>) featType(<featData>) `featType<-`(<ANY>) `featType<-`(<featData>) `featType<-`(<list>) `featType<-`(<giotto>) objName(<ANY>) objName(<list>) objName(<nameData>) objName(<giottoPoints>) objName(<giottoLargeImage>) objName(<giottoImage>) `objName<-`(<list>) `objName<-`(<nameData>) `objName<-`(<giottoImage>) `objName<-`(<giottoLargeImage>) `objName<-`(<giottoPoints>) prov(<provData>) `prov<-`(<provData>): Giotto schema

spatIDs(<giotto>) spatIDs(<exprObj>) spatIDs(<spatLocsObj>) spatIDs(<cellMetaObj>) spatIDs(<spatialNetworkObj>) spatIDs(<dimObj>) spatIDs(<giottoPolygon>) `spatIDs<-`(<giottoPolygon>) spatIDs(<spatEnrObj>) spatIDs(<nnNetObj>) featIDs(<giotto>) featIDs(<exprObj>) featIDs(<featMetaObj>) featIDs(<giottoPoints>) featIDs(<spatEnrObj>): Spatial and feature IDs

overlaps(<giottoPolygon>): overlaps-generic

Save/Load

Saving and loading of the Giotto Object

loadGiotto(): loadGiotto

saveGiotto(): saveGiotto

reconnectGiottoImage(): Reconnect images with dead pointers

As

As coercion functions

as.list(<giotto>): Coerce to a list

as.points(<data.frame>) as.points(<spatLocsObj>): Coerce to SpatVector points

as.polygons(<data.frame>): Coerce to SpatVector polygons

as.data.table(<SpatVector>) as.data.table(<giottoPolygon>) as.data.table(<giottoPoints>): Coerce to data.table

as.matrix(<spatLocsObj>) as.matrix(<nnNetObj>): Coerce to matrix

as.character(<giottoImage>) as.character(<svkey>) as.character(<giottoLargeImage>): Create a text representation of an object

as.sp(<sf>) as.sp(<SpatVector>) as.sp(<stars>) as.sp(<Spatial>) as.sp(<giottoPolygon>) as.sp(<giottoPoints>) as.sf(<SpatVector>) as.sf(<Spatial>) as.sf(<stars>) as.sf(<sf>) as.sf(<giottoPolygon>) as.sf(<giottoPoints>) as.stars(<SpatVector>) as.stars(<sf>) as.stars(<Spatial>) as.stars(<stars>) as.stars(<giottoPolygon>) as.stars(<giottoPoints>) as.terra(<SpatVector>) as.terra(<sf>) as.terra(<stars>) as.terra(<Spatial>) as.terra(<giottoPolygon>) as.terra(<giottoPoints>): R spatial conversions

Python

Giotto python environment

checkGiottoEnvironment() installGiottoEnvironment() removeGiottoEnvironment() set_giotto_python_path(): Giotto python environment

checkPythonPackage(): Check Python Package Installation

Coordinate stitching

stitchFieldCoordinates(): stitchFieldCoordinates

stitchTileCoordinates(): stitchTileCoordinates

Images

Image tools

stitchGiottoLargeImage(): Stitch multiple giottoLargeImage objects into a single giottoLargeImage object

convertGiottoLargeImageToMG(): convertGiottoLargeImageToMG

estimateImageBg(): estimateImageBg

distGiottoImage(): Plot distribution of image intensity values

density(<giottoLargeImage>): Density plot

hist(<giottoLargeImage>): Histogram

to_simple_tif() ometif_to_tif(): Convert Specialized TIF Formats to Basic TIF

tif_metadata() ometif_metadata(): Read Metadata of a Specialized tif

reconnect(<giottoAffineImage>) reconnect(<giottoLargeImage>) reconnect(<giottoImage>): Reconnect a GiottoClass object

changeImageBg(): changeImageBg

writeGiottoLargeImage(): writeGiottoLargeImage

updateGiottoImage(): updateGiottoImage

updateGiottoImageMG(): updateGiottoImageMG

updateGiottoLargeImage(): updateGiottoLargeImage

add_img_array_alpha(): Add alpha channel to image array

History

Functions for logging Giotto Object history

objHistory(): Giotto object history

update_giotto_params(): Update giotto parameters

showProcessingSteps(): showProcessingSteps

Utilities

Utility functions that are used in other code

polygon_to_raster(): Convert polygon to raster

smoothGiottoPolygons(): smoothGiottoPolygons

doDeferred(<giottoAffineImage>): Perform deferred/lazy operations

Deprecated

Deprecated and/or less supported older functions. Some of these functions are here for compatibility and internal purposes.

getSpatialGrid(): Get spatial grid

get_distance(): get_distance

get_multiomics(): Get multiomics integration results

createSpatialDefaultGrid(): createSpatialDefaultGrid

createSpatialGrid(): createSpatialGrid

setSpatialGrid(): Set spatial grid

set_multiomics(): Set multiomics integration results

triGrid() orthoGrid(): Spatial grids

cropGiottoLargeImage(): Crop a giotto largeImage object

plotGiottoImage(): Plot a giotto image object

showGiottoSpatGrids(): showGiottoSpatGrids

showGrids(): Show Spatial Grids

showNetworks(): Show networks

addGiottoPoints() addGiottoPoints3D(): Add subcellular giotto points object to giotto object

addGiottoPolygons(): Add giotto polygons to giotto object

annotateSpatialGrid(): annotateSpatialGrid

annotate_spatlocs_with_spatgrid_2D(): annotate_spatlocs_with_spatgrid_2D

annotate_spatlocs_with_spatgrid_3D(): annotate_spatlocs_with_spatgrid_3D