Package index • SPATA2

Around the SPATA2 object These functions generate the SPATA2 object you will work with throughot this and other platforms.
Initiation The initiation functions create a SPATA2 object from scratch or with standardized output from different platforms.
`initiateSpataObject()`	Initiate an object of class `SPATA2`
`initiateSpataObjectMERFISH()`	Initiate an object of class `SPATA2` from platform MERFISH
`initiateSpataObjectSlideSeqV1()`	Initiate an object of class `SPATA2` from platform SlideSeq
`initiateSpataObjectVisium()`	Initiate an object of class `SPATA2` from platform Visium
`initiateSpataObjectVisiumHD()`	Initiate an object of class `SPATA2` from platform VisiumHD
`initiateSpataObjectXenium()`	Initiate an object of class `SPATA2` from platform Xenium
Transformation The transform-functions ensure compatibility between different platforms.
`asGiotto()`	Transform SPATA2 object to Giotto object
`asMolecularAssay()`	Transform miscellaneous objects to MolecularAssay objects
`asSPATA2()`	Transform miscellaneous objects to SPATA2 objects
`asSeurat()`	Transform SPATA2 object to Seurat object
`asSingleCellExperiment()`	Transform SPATA2 object to SingleCellExperiment object
`asSummarizedExperiment()`	Transform SPATA2 object to SummarizedExperiment object
Loading, Downloading and Saving Some handy functions that make saving and loading corresponding objects more convenient.
`loadExampleObject()`	Load example SPATA2 object
`loadSpataObject()`	Load SPATA2 object
`saveSpataObject()`	Save SPATA2 object with a default directory
`downloadSpataObject()`	Download a SPATA2 object
`downloadSpataObjects()`	Download and save several SPATA2 objects
Object Subsetting & Manipulation Miscellaneous subsetting and renaming options.
`cropSpataObject()`	Crop SPATA2 object
`filterSpataObject()`	Subset SPATA2 object with logical expressions
`reduceSpataObject()`	Reduce SPATA2 object
`reduceResolutionVisiumHD()`	Reduce resolution for Visium HD data
`renameSpataObject()`	Rename SPATA2 object
`splitSpataObject()`	Split SPATA2 object
`subsetSpataObject()`	Subset SPATA2 object with barcodes
`updateSpataObject()`	Update SPATA2 object
Object Manipulation
Add Content to SPATA2 object The add-functions let you add content to the `SPATA2` object savely.
`addFeatures()`	Add meta variables for observations
`addInnerBorder()`	Add holes to spatial annotations
`addMetaDataMol()`	Add meta variables for molecular data
`addMetaDataObs()`	Add meta variables for observations
`addMoleculeCoordinates()`	Add molecule coordinates
`addProcessedMatrix()`	Add a processed matrix
`addGeneSet()` `addMetaboliteSet()` `addProteinSet()` `addSignature()`	Add molecular signature
`addSpatialAnnotation()`	Add a spatial annotation with data input
`addSpatialTrajectory()`	Add a spatial trajectory with data input
Create Content Create miscellaneous content and/or data containers.
`createHistoImage()`	Create an object of class `HistoImage`
`createMolecularAssay()`	Create and add an object of class `MolecularAssay`
`createSpatialData()` `createSpatialDataMERFISH()` `createSpatialDataSlideSeqV1()` `createSpatialDataVisium()` `createSpatialDataVisiumHD()` `createSpatialDataXenium()`	Create an object of class `SpatialData` from raw output
`createSpatialMethod()`	Create an object of class `SpatialMethod`
`createSpatialSegmentation()`	Interactive sample segmentation
`createSpatialTrajectories()`	Create and add spatial trajectories interactively
Process Miscellaneous Content A collection of miscellaneous processing functions.
`identifyVariableMolecules()`	Identify molecules of high variability
`identifyPixelContent()`	Identify pixel content
`normalizeCounts()`	Normalize raw counts
Rename Content The rename-functions let you adjust the name of certain content with which you refer to it via arguments.
`renameGroups()` `renameTissueSection()`	Rename cluster/group names
`renameImage()`	Rename an image
`renameMetaFeatures()`	Rename features
`renameMolecularAssay()`	Rename molecular assay
`renameSpataObject()`	Rename SPATA2 object
`renameSpatialAnnotation()`	Rename a spatial annotation
`renameSpatialTrajectory()`	Rename a spatial trajectory.
Set Content The set-functions let you set the content of specific slots.
`setDefault()`	Set object specific default
`setImageDir()`	Set image directory
`setMetaVarDf()`	Set molecular meta data.frame
`setScaleFactor()`	Set scale factors
`setSpataDir()`	Set SPATA2 directory
Availability Checks A collection of functions that check availability of processing steps and return logical values. (This is a subset of all related functions.)
`containsAssay()`	Check availability of an assay
`containsCCD()`	Check availability of center to center distance
`containsCNV()`	Check availability CNV results
`containsCells()`	Check availability of cells
`containsHistoImages()`	Check availability of image containers
`containsImage()`	Check availability of an image
`containsInnerBorders()`	Check for inner borders in a spatial annotation
`containsMethod()`	Check availability of specific spatial methods (platforms)
`containsModality()`	Check availability of molecular modality
`containsMoleculeCoordinates()`	Check availability molecule coordinates
`containsPixelContent()`	Check availability pixel content
`containsScaleFactor()`	Check availability of specific scale factors
`containsSpatialAnnotations()`	Check availability of spatial annotations
`containsSpatialData()`	Checks availability of a SpatialData object
`containsSpatialOutliers()`	Check if spatial outliers exist
`containsSpots()`	Check availability of spots
`containsTissueOutline()`	Check availability of tissue outline
Built-in Data A list of data built into SPATA2.
`cnv_ref`	A list of reference data for copy number variation analysis (CNV)
`cnv_regions_df`	A data.frame necessary for cnv-analysis. Contains information about start and end points of chromosomes.
`example_data`	Data required for reproducible examples in SPATA2 tutorials.
`gene_pos_df`	A data.frame necessary for cnv-analysis. Contains information about the gene positions on chromosomes. Contains the following variables:
`regexes`	Regular Expressions for Data Validation and Parsing
`signatures`	The default collection of frequently used signatures
`visium_spots`	A list of a slot named VisiumSmall, which contains a list of data.frames of all barcoded spots of 6.5mm capture area and a slot named VisiumLarge which a list of data.frames that contain the barcoded spots of the 11mm capture area.
Activate Content Functions to manage object specific defaults.
`activateAssay()` `activeAssay()`	Default assay name
`activeImage()` `activateImage()` `activateImageInt()`	Default image name
`activateMatrix()` `activeMatrix()`	Default matrix name
Counting Functions that quantify the abundance of specific ascpects in the `SPATA2` object.
`nImages()`	Number of images
`nGenes()` `nMolecules()` `nMetabolites()` `nProteins()`	Number of molecules
`nObs()`	Number of observations
`nSpatialAnnotations()`	Number of spatial annotations
`nSpatialTrajectories()` `nTrajectories()`	Number of spatial trajectories
Extract Data
Copy Number Variations Functions to extract CNV related content.
`getChrRegionsDf()`	Obtain chromosome information
`getCnvFeatureNames()`	Obtain features names under which cnv-analysis results are stored.
`getCnvGenesDf()`	Obtain CNV results by gene
`getCnvResults()`	Obtain CNV results
Molecular Data Functions to extract molecular data and particularly names of molecular variables.
`getAssay()`	Obtain molecular assay
`getAssayModalities()` `getAssayNames()`	Obtain assay names/modalites
`getGenePosDf()`	Obtain gene CNV information
`getGeneSet()` `getMetaboliteSet()` `getProteinSet()` `getSignature()`	Obtain molecular signature
`getGeneSetList()` `getMetaboliteSetList()` `getProteinSetList()` `getSignatureList()`	Obtain molecular signatures
`getGeneSets()` `getMetaboliteSets()` `getProteinSets()` `getSignatureNames()`	Obtain molecular signature names
`getGeneSetOverview()` `getMetaboliteOverview()` `getProteinSetOverview()` `getSignatureOverview()`	Overview about the current signature collection
`getCountMatrix()`	Obtain raw counts
`getMatrix()` `getMatrices()`	Obtain a data matrix
`getMatrixNames()`	Obtain matrix names
`getProcessedMatrix()`	Obtain processed data matrix
`getProcessedMatrixNames()`	Obtain names of processed matrices
`getMetaVarDf()`	Obtain molecular meta data.frame
`getModality()`	Obatin molecular modality
`getMoleculeCoordinates()`	Obtain molecule coordinates
`getMoleculeTypeList()`	Obtain a list of molecules
`getGenes()` `getMetabolites()` `getMolecules()` `getProteins()`	Obtain molecule names
`getSignatureTypeList()`	Obtain a list of signatures
`getVariableMolecules()`	Obtain molecules of high variability
Spatial Coordinates Functions to extract coordinates of observations.
`getCoordsCenter()`	Obtain coordinate center
`getCoordsDf()`	Obtain coordinates
`getCoordsDfSA()` `getCoordsDfST()`	Relate points to spatial annotations
`getCoordsMtr()`	Obtain coordinates matrix
`getCoordsRange()`	Obtain coordinate range
Dimensional Reduction Functions to extract dimensional reduction results.
`getDimRedDf()` `getPcaDf()` `getPcaMtr()` `getTsneDf()` `getUmapDf()`	Obtain dim red data.frame
Features & Grouping Functions to extract grouping related variables and names.
`getCnvFeatureNames()`	Obtain features names under which cnv-analysis results are stored.
`getFeatureNames()` `getMetaNames()`	Obtain metadata column names
`getGroupingOptions()`	Obtain variable names that group data points
`getGroupNames()`	Obtain group names a grouping variable contains
`getMetaDf()`	Obtain meta data.frame for observations
`getSpatSegmVarNames()`	Obtain segmentation variable names
Differential Expression Analysis Functions to extract DEA related content.
`getDeaGenes()` `getDeaResultsDf()`	Obtain DEA results
Gene Set Enrichment Analysis Functions to extract GSEA related content.
`getGseaDf()`	Obtain enrichment data.frame
`getGseaResults()`	Obtain enrichment results
Spatial Gradient Screening Functions to extract SGS related content.
`getSgsResultsDf()`	Obtain spatial gradient screening results
`getSgsResultsVec()`	Obtain spatial gradient screening results
`getSasDf()`	Obtain spatial annotation screening data.frame
`getStsDf()`	Obtain spatial trajectory screening data.frame
Image Functions to extract image related content.
`getHistoImage()` `getHistoImageRef()`	Obtain HistoImage object
`getImage()`	Obtain image
`getImageCenter()`	Obtain image center
`getImageDf()`	Obtain image as a data.frame
`getImageDims()` `getImageRange()`	Obtain image dimensions/ranges
`getImageDir()` `getImageDirectories()`	Obtain directory to image
`getImageNames()`	Obtain names of registered images
`getImageSectionsByBarcode()`	Obtain image sections by barcode
`getImageTransformations()`	Obtain image transformation instructions
`getPixelDf()`	Obtain pixel data.frame
`getPixelScaleFactor()`	Obtain scale factor for pixel to SI conversion
Spatial Annotations Functions to extract data related to spatial annotations.
`getSpatialAnnotation()`	Obtain a SpatialAnnotation object
`getSpatialAnnotations()`	Obtain list of SpatialAnnotation objects
`getSpatAnnArea()`	Obtain area of spatial annotation
`getSpatAnnBarcodes()`	Obtain barcodes by spatial annotations
`getSpatAnnCenter()` `getSpatAnnCenters()`	Obtain center of a spatial annotation
`getSpatAnnCenterBcsp()`	Obtain center data point
`getSpatAnnIds()`	Obtain IDs of spatial annotations
`getSpatAnnOutlineDf()`	Obtain the outline of a spatial annotation
`getSpatAnnRange()`	Obtain spatial annotations range
`getSpatAnnSf()`	Obtain the outline of a spatial anontation
`getSpatAnnTags()`	Obtain spatial annotation tags
Spatial Trajectories Functions to extract data related to spatial trajectories.
`getProjectionDf()`	Obtain trajectory projection
`getSpatialTrajectory()` `getSpatialTrajectories()`	Obtain SpatialTrajectory objects
`getSpatialTrajectoryIds()`	Obtain trajectory IDs
`getTrajectoryLength()`	Obtain length of spatial trajectory
`getTrajectorySegmentDf()`	Obtain trajectory course
`getTrajectoryWidth()`	Obtain trajectory width
Tissue, Tissue Outline & Spatial Measures Functions to extract tissue related data.
`getCaptureArea()`	Obtain capture area
`getCCD()`	Obtain center to center distance
`getDefaultUnit()`	Obtain default unit
`getSpatialMethod()`	Obtain spatial method
`getTissueArea()`	Obtain tissue area size
`getTissueOutlineCentroid()`	Obtain tissue outline centroid
`getTissueOutlineDf()`	Obtain the outline of tissue sections
`getTissueSections()`	Obtain the names of tissue sections
Miscellaneous Functions to extract miscellaneous types of data.
`getBarcodes()`	Obtain barcodes
`getDefault()` `getDefaultInstructions()`	Obtain default argument inputs
`getLogfileDf()`	Obtain object logfile data.frame
`getMethodSpecifics()`	Obtain platform details
`getPlatform()`	Obtain platform name
`getSampleName()`	Obtain name of SPATA2 object
`getScaleFactor()`	Obtain scale factors
`getSpataDf()`	Obtain a data.frame of observations
`getSpataDir()`	Obtain SPATA2 object directory
`getSpatialData()`	Obtain SpatialData object
`getVariableNames()`	Obtain variable names of the SPATA2 object
Remove Content Remove miscellaneous kinds of data from a SPATA2 object.
`registerImage()` `removeImage()`	Register or remove images
`removeMetaFeatures()`	Remove meta features
`removeGenes()` `removeGenesMitochondrial()` `removeGenesRibosomal()` `removeGenesStress()` `removeGenesZeroCounts()` `removeMolecules()`	Remove molecules from the SPATA2 object
`removeObs()` `removeObsZeroCounts()`	Remove observations
`removeProcessedMatrix()`	Remove a processed matrix
`removeSignatures()`	Remove molecular signatures
`removeSpatialAnnotations()`	Remove spatial annotations
`removeSpatialOutliers()`	Remove spatial outliers
`removeSpatialTrajectories()`	Remove spatial trajectories
`removeTissueFragments()`	Remove data points from tissue fragments
Management of Grouping Variables Functions to change grouping variables.
`mergeGroups()`	Lump groups together
`dissolveGroups()`	Dissolve groups in a SPATA2 object
`renameGroups()` `renameTissueSection()`	Rename cluster/group names
`relevelGroups()`	Relevel groups of grouping variable
Spatial Annotation Handling Functions to create and work with spatial annotations.
Create Spatial Annotations
`addSpatialAnnotation()`	Add a spatial annotation with data input
`barcodesToSpatialAnnotation()`	Create spatial annotations from a list of barcodes
`createGroupAnnotations()`	Create spatial annotations from a group of data points
`createImageAnnotations()`	Create spatial annotations based on histo-morphological features
`createNumericAnnotations()`	Create spatial annotations based on numeric values
Manipulate Spatial Annotations
`centerSpatialAnnotation()`	Center the borders of a spatial annotation
`expandSpatialAnnotation()`	Expand the outline of spatial annotations
`mergeSpatialAnnotations()`	Merge spatial annotations
`renameSpatialAnnotation()`	Rename a spatial annotation
`rotateSpatialAnnotation()`	Rotate the outline of a spatial annotation
`shiftSpatialAnnotation()`	Shift the borders of a spatial annotation
`smoothSpatialAnnotation()`	Smooth the border of a spatial annotation
`tagSpatialAnnotations()`	Tag spatial annotations
Use Spatial Annotations
`mapSpatialAnnotationTags()`	Spatial annotation and barcode intersection
`spatialAnnotationToGrouping()`	Convert spatial annotation to grouping variable
Image handling and Image-Coordinate Alignment Functions to work with and ensure alignment between images and coordinates of observations.
`flipAll()` `flipCoordinates()` `flipCoordsDf()` `flipImage()` `flipSpatialAnnotations()` `flipSpatialTrajectories()`	Mirror invert image and coordinates
`loadImage()` `loadImages()`	Load image slot content
`refImage()`	Obtain name of reference iamge
`registerImage()` `removeImage()`	Register or remove images
`resizeImage()`	Resize image
`resetImageTransformations()`	Reset image transformations
`rotateAll()` `rotateImage()` `rotateCoordinates()` `rotateCoordsDf()` `rotateTissueOutlineDf()` `rotateSpatialAnnotations()` `rotateSpatialTrajectories()`	Rotate image and coordinates
`rotateSpatialAnnotation()`	Rotate the outline of a spatial annotation
`unloadImage()` `unloadImages()`	Unload image slot content
`writeImage()`	Write image to disk
Join Information These functions access the information of interest, perform additional customized computations and join it as additional variables to already existing data.frames in a tidy-data fashion.
`joinWithPca()` `joinWithTsne()` `joinWithUmap()`	Join barcodes with additional variables
`joinWithVariables()`	Join data with variables
Implemented Algorithms These functions perform calculations that might take some time. The results are stored inside the SPATA2 object.
`computeCaptureArea()`	Compute capture area
`computeCnvByChrArm()`	Compute CNV by chromosome arm
`computeCountPercentage()`	Compute count percentage
`computeMetaFeatures()`	Compute meta features
`computePixelScaleFactor()`	Compute pixel scale factor
`runBayesSpaceClustering()`	Clustering with BayesSpace
`runCNV()` `runCnvAnalysis()`	Identify large-scale chromosomal copy number variations
`runDEA()` `runDeAnalysis()`	Differential expression analysis (DEA)
`runGSEA()`	Compute gene set enrichment
`runKmeansClustering()`	Clustering with Kmeans
`runNearestNeighborClustering()`	Clustering with nearest neighbor search
`runPCA()` `runPca()`	Run Principal Component Analysis
`getSparkxGeneDf()` `getSparkxGenes()` `getSparkxResults()` `runSPARKX()`	Identify spatially significant features with SPARKX
`runSeuratClustering()`	Clustering with Seurat
`runTSNE()` `runTsne()`	Run t-Stochastic Neighbour Embedding
`runUMAP()` `runUmap()`	Run Uniform Manifold Approximation and Projection
`compute_img_scale_fct()`	Compute scale factor of two images
Tissue Outline & Tissue Sections Functions that incorporate the spatial dimensions and outline of the tissue using data points or images as information.
`distToEdge()`	Distance to edge of tissue section
`identifyPixelContent()`	Identify pixel content
`identifyTissueOutline()`	Identify tissue outline
`identifySpatialOutliers()`	Identify spatial outliers
`mergeTissueSections()`	Merge tissue sections
`mergeWithTissueOutline()`	Integrate tissue outline in spatial annotation
`renameGroups()` `renameTissueSection()`	Rename cluster/group names
`useVarForTissueOutline()`	Use specified variable for tissue outline
`whichTissueSection()`	Tissue section belonging of spatial annotations
Miscellaneous Spatial Functions
`add_dbscan_variable()` `add_tissue_section_variable()`	Add tissue section variable to coordinate data.frame
`add_edge_variable()`	Add edge variable to coordinate data.frame
`add_grid_variable()`	Add grid variable to coordinate data.rame
`buffer_area()`	Buffer area
`identify_obs_in_polygon()` `identify_obs_in_spat_ann()`	Identify observations inside a polygon
`include_tissue_outline()`	Include spatial extent of tissue sections in analysis
`intersect_polygons()`	Test polygon intersection
`map_to_tissue_section()`	Map observations to tissue sections
`merge_intersecting_polygons()`	Merge polygons
Spatial Gradient Screening Functions around Spatial Trajectory Screening and Image Annotation Screening.
`spatial_gradient_screening()`	Low level implementation of the spatial gradient screening algorithm
`spatialAnnotationScreening()`	The Spatial Annotation Screening algorithm
`spatialTrajectoryScreening()`	The Spatial Trajectory Screening algorithm
`getStsDf()`	Obtain spatial trajectory screening data.frame
`getSasDf()`	Obtain spatial annotation screening data.frame
`plotSasBarplot()`	Plot SAS barplot
`plotSasDensityplot()`	Plot SAS densityplot
`plotSasHeatmap()`	Plot SAS heatmap
`plotSasLineplot()`	Plot SAS lineplot
`plotSasRidgeplot()`	Plot SAS rideplot
Spatial Measures Functions to work with spatial measures in SI units.
`are_all_area_or_dist()` `are_all_dist()`	Test area or distance input
`as_meter()` `as_meter2()` `as_micrometer()` `as_micrometer2()` `as_millimeter()` `as_millimeter2()` `as_nanometer()` `as_nanometer2()` `as_pixel()` `as_unit()` `as_centimeter()` `as_centimeter2()` `as_decimeter()` `as_decimeter2()`	Transform distance and area values
`as_SPATA2_dist()`	Distance transformation
`extract_unit()`	Extract distance units
`extract_value()`	Extract distance value
`is_area()` `is_area_pixel()` `is_area_si()`	Test area input
`is_dist()` `is_dist_si()` `is_dist_pixel()`	Test distance input
`is_unit_area()`	Test unit of area input
`is_unit_dist()`	Test unit of length input
S4 Classes The S4 classes SPATA2 uses to abstract concepts of spatial multi-omic experiments.
`GroupAnnotation-class` `GroupAnnotation`	The `GroupAnnotation` - Class
`HistoImage-class` `HistoImage`	The `HistoImage` - Class
`ImageAnnotation-class` `ImageAnnotation`	The `ImageAnnotation` - Class
`MolecularAssay-class` `MolecularAssay`	The `MolecularAssay` - Class
`NumericAnnotation-class` `NumericAnnotation`	The `NumericAnnotation` - Class
`SPATA2-class` `SPATA2`	The `SPATA2` - class
`SpatialAnnotation-class` `SpatialAnnotation`	The `SpatialAnnotation` - Class
`SpatialAnnotationScreening-class` `SpatialAnnotationScreening`	The `SpatialAnnotationScreening` - Class
`SpatialData-class` `SpatialData`	The `SpatialData` - Class
`SpatialGradientScreening-class` `SpatialGradientScreening`	The `SpatialGradientScreening` - Class
`SpatialMethod-class` `SpatialMethod`	The `SpatialMethod` - Class
`SpatialTrajectory-class` `SpatialTrajectory`	The `SpatialTrajectory` - Class
`SpatialTrajectoryScreening-class` `SpatialTrajectoryScreening`	The `SpatialTrajectoryScreening` - Class
Platforms Variables that have been defined as objects of class `SpatialMethod` to store information related to the spatial platforms.
`MERFISH`	MERFISH Spatial Method
`VisiumSmall`	VisiumSmall Spatial Method
`VisiumHD`	VisiumHD Spatial Method
`VisiumLarge`	VisiumLarge Spatial Method
`SlideSeqV1`	SlideSeqV1 Spatial Method
`Xenium`	Xenium Spatial Method
Visualization
Copy Number Variation
`plotCnvHeatmap()`	Plot CNV Heatmap
`plotCnvLineplot()`	Plot CNV Lineplot
DEA & GSEA Visualize the results of differential expression analysis and gene set enrichment analysis.
`plotDeaDotPlot()`	Plot DEA results via dot plots
`plotDeaHeatmap()`	Plot DEA results via heatmaps
`plotDeaVolcano()` `plotDeaVolcano1v1()`	Plot DEA results via volcano plots
`plotGseaDotPlot()`	Plot GSEA results via dot plots
Dimensional Reduction Visualize the barcode spots in a reduced dimension fashion.
`plotPCA()` `plotPca()` `plotTSNE()` `plotTsne()` `plotTsneComparison()` `plotUMAP()` `plotUmap()` `plotUmapComparison()`	Plot dimensional reduction
`plotPcaElbow()`	Plot PCA Elbow Plot
`plotPcaVariation()`	Plot PCA Variation
ggpLayer and other gg objects Add ggroto objects to ggplot2 plots.
`ggpInit()`	Initiate ggplot2 layering
`ggpLayerAxesClean()`	Display clean axes
`ggpLayerAxesSI()`	Display axes with SI units of length
`ggpLayerCaptureArea()`	Add capture area to surface plot
`ggpLayerColorGroupScale()`	Add group specific color spectrum
`ggpLayerExprEstimatesSAS()`	Add SAS expression estimates
`ggpLayerFrame()` `ggpLayerFixFrame()`	Fix ggplot frame
`ggpLayerFrameByCoords()` `ggpLayerFrameByImage()`	Set plot limits
`ggpLayerGridVisiumHD()`	Add a grid to VisiumHD surface plots
`ggpLayerGroupOutline()`	Add group outline
`ggpLayerHorizonSAS()`	Add SAS screening horizon
`ggpLayerImage()`	Add histology image
`ggpLayerPoints()`	Add the observations to the surface plot
`ggpLayerRect()`	Add a rectangular to the plot
`ggpLayerScaleBarSI()`	Add a scale bar in SI units
`ggpLayerScreeningDirectionSAS()`	Add SAS screening direction
`ggpLayerSpatAnnOutline()`	Add outline of spatial annotations
`ggpLayerSpatAnnPointer()`	Add pointer towards spatial annotations
`ggpLayerSpatAnnRect()`	Add a rectangular around an spatial annotation
`ggpLayerSpatialTrajectories()`	Add spatial trajectories
`ggpLayerThemeCoords()`	Add coordinates theme
`ggpLayerTissueOutline()`	Add a hull outlining the tissue
`ggpLayerTrajectoryFrame()`	Add the screening frame of a spatial trajectory
`ggpLayerZoom()`	Set plot limits manually
`theme_lineplot_gradient()` `theme_ridgeplot_gradient()` `theme_trajectory_fit()` `theme_transparent()`	ggplot2 themes
`labsNone()` `legendBottom()` `legendColor()` `legendLeft()` `legendNone()` `legendRight()` `legendTop()`	ggplot2 basic manipulation
geoms
`geom_point_fixed()`	Points (fixed size ~ window ratio)
`geom_segment_fixed()`	Segments (fixed size ~ window ratio)
`geom_text_fixed()`	Text (fixed size ~ window ratio)
Image
`plotImage()`	Plot histology image
`plotImages()`	Plot histology images
`plotImageBase()`	Plot image with R base plotting
`plotImageMask()` `plotPixelContent()`	Plot pixel content
Miscellaneous Visualize a variety of aspects.
`plotLoglik()`	Plot Bayes Space logliks
`plotScatterplot()`	Plot numeric variables as a scatterplot
`showColors()` `showColorPalettes()` `showColorSpectra()`	Show color palettes and spectra
`showModels()`	Show spatial gradient screening models
Spatial Gradient
`plotExprVsDistSA()` `plotExprVsDistST()`	Plot expression as a function of distance to a spatial references
`plotSpatialAnnotations()`	Plot spatial annotations
`plotSpatialTrajectories()`	Plot spatial trajectories
`plotSasBarplot()`	Plot SAS barplot
`plotSasDensityplot()`	Plot SAS densityplot
`plotSasHeatmap()`	Plot SAS heatmap
`plotSasLineplot()`	Plot SAS lineplot
`plotSasRidgeplot()`	Plot SAS rideplot
`plotStsBarplot()`	Plot STS barplot
`plotStsHeatmap()`	Plot STS heatmap
`plotStsLineplot()` `plotStsRidgeplot()`	Plot STS line- and ridgeplot
Statistics
`plotBarchart()`	Plot distribution of discrete variables
`plotBoxplot()` `plotDensityplot()` `plotHistogram()` `plotRidgeplot()` `plotVioBoxplot()` `plotViolinplot()`	Plot numeric distribution and statistical tests
`plotMosaicplot()`	Plot mosaic plot
`plotRiverplot()`	Plot riverplots
`plotStatisticsInteractive()`	Plot distribution of variables interactively
Surface Plots & 2D data
`plotSurface()` `plotSurfaceInteractive()`	Plot the surface of the sample
`plotSurfaceBase()`	Plot surface with R base plotting
`plotSurfaceComparison()`	Plot several surface plots colored by numeric variables
`plotSurfaceSAS()`	Plot screening area of SAS set up
`plotSurfaceSC()`	Plot single cells on surface
`plotMolecules2D()`	Plot molecules in 2D space
Miscellaneous Functions
`currentSpata2Version()`	The current version of SPATA2
`deprecatedInfo()`	Information about deprecated aspects
`is_outlier()`	Check for outliers in a numeric vector
`isSPATA2()`	General test for SPATA2 object
`make_binary_image()`	Convert Image to Binary with Flexible Thresholding
`model_ascending()` `model_descending()`	Generate model-based ascending or descending sequence
`model_peak()` `model_trough()`	Model a peaking pattern
`obsUnit()`	The observational unit
`recAlpha()` `recDbscanEps()` `recDbscanMinPts()` `recSgsRes()`	Platform dependent input recommendations
`read_coords()` `read_coords_merfish()` `read_coords_slide_seq_v1()` `read_coords_visium()` `read_coords_xenium()`	Read coordinate data.frames
`read_matrix_from_folder()`	Read Matrix from Folder
`transform_coords()`	Transform coordinates
`transform_image()`	Transform image
`unwindAggregation()`	Map aggregated to pre-aggregated barcodes

Reference

Around the SPATA2 object

Initiation

Transformation

Loading, Downloading and Saving

Object Subsetting & Manipulation

Object Manipulation

Add Content to SPATA2 object

Create Content

Process Miscellaneous Content

Rename Content

Set Content

Availability Checks

Built-in Data

Activate Content

Counting

Extract Data

Copy Number Variations

Molecular Data

Spatial Coordinates

Dimensional Reduction

Features & Grouping

Differential Expression Analysis

Gene Set Enrichment Analysis

Spatial Gradient Screening

Image

Spatial Annotations

Spatial Trajectories

Tissue, Tissue Outline & Spatial Measures

Miscellaneous

Remove Content

Management of Grouping Variables

Spatial Annotation Handling

Create Spatial Annotations

Manipulate Spatial Annotations

Use Spatial Annotations

Image handling and Image-Coordinate Alignment

Join Information

Implemented Algorithms

Tissue Outline & Tissue Sections

Miscellaneous Spatial Functions

Spatial Gradient Screening

Spatial Measures

S4 Classes

Platforms

Visualization

Copy Number Variation

DEA & GSEA

Dimensional Reduction

ggpLayer and other gg objects

geoms

Image

Miscellaneous

Spatial Gradient

Statistics

Surface Plots & 2D data

Miscellaneous Functions