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()

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

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

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