Function reference • SPATA

Around objects Functions that affect the spata-object as a whole.
General
`initiateSpataObject_10X()`	Initiate a spata-object
`loadSpataObject()` `saveSpataObject()`	Load and save a spata-object
`validateSpataObject()`	Validate a spata object
`subsetSpataObject()`	Subset a spata-object
Gene-set Functions that affect the gene-set data.frame.
`adjustGeneSetDf()`	Filter gene-set data.frame
`saveGeneSetDf()`	Save a gene set data.frame
Compile objects Functions that compile objects of other R-packages
`compileCellDataSet()`	Initiate monocle3 analysis
`compileSeuratObject()`	Initiate Seurat analysis
Extract information SPATA invites you to extract your analysis. get-functions let you access every imaginable aspect of information conveniently.
Spatial & Spatial Segments
`getCoordinates()` `getCoordinatesSegment()`	Obtain spatial coordinates
`getSegmentNames()`	Obtain segment names
`getDimRedData()` `getUmapData()` `getTsneData()`	Obtain dimensional reduction data
Features
`getFeatureNames()`	Obtain feature names
`getFeatureData()`	Obtain feature data
`getFeatureVariables()`	Obtain a feature variable
Genes & Gene-sets
`getGenes()` `getGenesInteractive()`	Obtain gene names
`getGeneSetOverview()`	Overview about the current gene sets
`getGeneSets()` `getGeneSetsInteractive()`	Obtain gene set names
Data matrices
`getBarcodes()`	Obtain barcodes of a sample
`getExpressionMatrix()` `getCountMatrix()`	Obtain count and expression matrix
Trajectories
`getTrajectoryNames()`	Obtain trajectory names
`getTrajectoryObject()`	Obtain trajectory object
`getTrajectoryDf()`	Obtain a summarized trajectory data.frame
Create, Add & Discard Information SPATA invites you to extract your analysis and to add the results of your analysis. Constant change of the object’s content is therefore inevitable. The following functions serve as handy, helping hands to add SPATA-extern content to the object without disturbing it’s integrity regarding SPATA-intern processes.
Create content interactively The create-functions always open an interactive application in which the content to be added needs to be created at first.
`createSegmentation()`	Spatial Segmentation
`createTrajectories()`	Spatial Trajectories
Add content The add-functions let you add content to the spata-object savely.
`addFeatures()`	Add a new feature
`addGeneSet()` `addGeneSetsInteractive()`	Add a new gene set
`addUmapData()` `addTsneData()`	Add dimensional reductions
Discard content The discard-functions let you delete unwanted information savely.
`discardGeneSets()`	Discard gene sets
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.
`joinWith()` `joinWithFeatures()` `joinWithGenes()` `joinWithGeneSets()` `joinWithVariables()`	Join barcodes with additional variables
Analysis
Trajectories
`assessTrajectoryTrends()` `assessTrajectoryTrends2()`	Trajectory trend analysis
Miscellaneous
`findDE()`	Find marker genes
`findMonocleClusters()`	Cluster sample via monocle3
Process & Examine
`filterDE()`	Postprocess de-results
`filterTrends()`	Filter variables of a certain trend
`examineClusterResults()`	Examine clustering results
`examineDeResults()`	Examine differentially expression results
`examineTrajectoryAssessment()`	Examine trajectory-moddeling results
Visualization
Surface Plots Visualize the barcode-spots information with a spatial dimension.
`plotSurface()` `plotSurface2()` `plotSurfaceInteractive()`	Plot the sample
`plotSurfaceComparison()` `plotSurfaceComparison2()`	Plot several surface plots at the same time
`plotSegmentation()`	Plot segmentation
Dimensional Reduction Visualize the barcode spots in a reduced dimension fashion.
`plotUMAP()` `plotTSNE()`	Plot dimensional reduction
Trajectory Visualize the barcode-spots information with a directional dimension.
`plotTrajectory()`	Plot trajectory
`plotTrajectoryFeatures()` `plotTrajectoryFeaturesDiscrete()` `plotTrajectoryGenes()` `plotTrajectoryGeneSets()`	Trajectory line plots
`plotTrajectoryFit()`	Display trajectory fit
`plotTrajectoryHeatmap()`	Expression dynamic in heatmap
Miscellaneous Visualize a variety of aspects.
`plotDistribution()` `plotDistribution2()`	Distribution of continuous values
`plotDistributionAcross()` `plotDistributionAcross2()`	Distribution of continuous values
`plotDistributionDiscrete()`	Distribution of discrete features
`plotFourStates()` `plotFourStates2()`	Gene set state plot
`plotDeHeatmap()`	Plot differentially expressed genes

Reference

Around objects

General

Gene-set

Compile objects

Extract information

Spatial & Spatial Segments

Features

Genes & Gene-sets

Data matrices

Trajectories

Create, Add & Discard Information

Create content interactively

Add content

Discard content

Join Information

Analysis

Trajectories

Miscellaneous

Process & Examine

Visualization

Surface Plots

Dimensional Reduction

Trajectory

Miscellaneous