Around the SPATA2 objectThese functions generate the SPATA2 object you will work with throughot this and other platforms. |
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InitiationThe initiation functions create a SPATA2 object from scratch or with standardized output from different platforms. |
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Initiate an object of class |
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Initiate an object of class |
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Initiate an object of class |
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Initiate an object of class |
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Initiate an object of class |
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Initiate an object of class |
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TransformationThe transform-functions ensure compatibility between different platforms. |
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Transform SPATA2 object to Giotto object |
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Transform miscellaneous objects to MolecularAssay objects |
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Transform miscellaneous objects to SPATA2 objects |
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Transform SPATA2 object to Seurat object |
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Transform SPATA2 object to SingleCellExperiment object |
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Transform SPATA2 object to SummarizedExperiment object |
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Loading, Downloading and SavingSome handy functions that make saving and loading corresponding objects more convenient. |
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Load example SPATA2 object |
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Load SPATA2 object |
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Save SPATA2 object with a default directory |
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Download a SPATA2 object |
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Download and save several SPATA2 objects |
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Object Subsetting & ManipulationMiscellaneous subsetting and renaming options. |
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Crop SPATA2 object |
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Subset SPATA2 object with logical expressions |
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Reduce SPATA2 object |
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Reduce resolution for Visium HD data |
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Rename SPATA2 object |
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Split SPATA2 object |
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Subset SPATA2 object with barcodes |
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Update SPATA2 object |
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Object Manipulation |
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Add Content to SPATA2 objectThe add-functions let you add content to the |
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Add meta variables for observations |
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Add holes to spatial annotations |
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Add meta variables for molecular data |
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Add meta variables for observations |
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Add molecule coordinates |
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Add a processed matrix |
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Add molecular signature |
Add a spatial annotation with data input |
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Add a spatial trajectory with data input |
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Create ContentCreate miscellaneous content and/or data containers. |
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Create an object of class |
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Create and add an object of class |
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Create an object of class |
Create an object of class |
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Interactive sample segmentation |
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Create and add spatial trajectories interactively |
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Process Miscellaneous ContentA collection of miscellaneous processing functions. |
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Identify molecules of high variability |
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Identify pixel content |
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Normalize raw counts |
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Rename ContentThe rename-functions let you adjust the name of certain content with which you refer to it via arguments. |
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Rename cluster/group names |
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Rename an image |
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Rename features |
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Rename molecular assay |
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Rename SPATA2 object |
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Rename a spatial annotation |
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Rename a spatial trajectory. |
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Set ContentThe set-functions let you set the content of specific slots. |
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Set object specific default |
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Set image directory |
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Set molecular meta data.frame |
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Set scale factors |
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Set SPATA2 directory |
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Availability ChecksA collection of functions that check availability of processing steps and return logical values. (This is a subset of all related functions.) |
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Check availability of an assay |
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Check availability of center to center distance |
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Check availability CNV results |
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Check availability of cells |
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Check availability of image containers |
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Check availability of an image |
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Check for inner borders in a spatial annotation |
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Check availability of specific spatial methods (platforms) |
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Check availability of molecular modality |
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Check availability molecule coordinates |
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Check availability pixel content |
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Check availability of specific scale factors |
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Check availability of spatial annotations |
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Checks availability of a SpatialData object |
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Check if spatial outliers exist |
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Check availability of spots |
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Check availability of tissue outline |
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Built-in DataA list of data built into SPATA2. |
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A list of reference data for copy number variation analysis (CNV) |
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A data.frame necessary for cnv-analysis. Contains information about start and end points of chromosomes. |
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Data required for reproducible examples in SPATA2 tutorials. |
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A data.frame necessary for cnv-analysis. Contains information about the gene positions on chromosomes. Contains the following variables: |
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Regular Expressions for Data Validation and Parsing |
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The default collection of frequently used signatures |
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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. |
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Activate ContentFunctions to manage object specific defaults. |
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Default assay name |
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Default image name |
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Default matrix name |
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CountingFunctions that quantify the abundance of specific ascpects in the |
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Number of images |
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Number of molecules |
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Number of observations |
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Number of spatial annotations |
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Number of spatial trajectories |
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Extract Data |
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Copy Number VariationsFunctions to extract CNV related content. |
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Obtain chromosome information |
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Obtain features names under which cnv-analysis results are stored. |
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Obtain CNV results by gene |
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Obtain CNV results |
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Molecular DataFunctions to extract molecular data and particularly names of molecular variables. |
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Obtain molecular assay |
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Obtain assay names/modalites |
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Obtain gene CNV information |
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Obtain molecular signature |
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Obtain molecular signatures |
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Obtain molecular signature names |
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Overview about the current signature collection |
Obtain raw counts |
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Obtain a data matrix |
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Obtain matrix names |
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Obtain processed data matrix |
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Obtain names of processed matrices |
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Obtain molecular meta data.frame |
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Obatin molecular modality |
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Obtain molecule coordinates |
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Obtain a list of molecules |
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Obtain molecule names |
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Obtain a list of signatures |
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Obtain molecules of high variability |
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Spatial CoordinatesFunctions to extract coordinates of observations. |
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Obtain coordinate center |
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Obtain coordinates |
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Relate points to spatial annotations |
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Obtain coordinates matrix |
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Obtain coordinate range |
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Dimensional ReductionFunctions to extract dimensional reduction results. |
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Obtain dim red data.frame |
Features & GroupingFunctions to extract grouping related variables and names. |
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Obtain features names under which cnv-analysis results are stored. |
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Obtain metadata column names |
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Obtain variable names that group data points |
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Obtain group names a grouping variable contains |
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Obtain meta data.frame for observations |
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Obtain segmentation variable names |
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Differential Expression AnalysisFunctions to extract DEA related content. |
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Obtain DEA results |
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Gene Set Enrichment AnalysisFunctions to extract GSEA related content. |
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Obtain enrichment data.frame |
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Obtain enrichment results |
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Spatial Gradient ScreeningFunctions to extract SGS related content. |
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Obtain spatial gradient screening results |
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Obtain spatial gradient screening results |
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Obtain spatial annotation screening data.frame |
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Obtain spatial trajectory screening data.frame |
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ImageFunctions to extract image related content. |
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Obtain HistoImage object |
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Obtain image |
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Obtain image center |
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Obtain image as a data.frame |
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Obtain image dimensions/ranges |
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Obtain directory to image |
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Obtain names of registered images |
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Obtain image sections by barcode |
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Obtain image transformation instructions |
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Obtain pixel data.frame |
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Obtain scale factor for pixel to SI conversion |
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Spatial AnnotationsFunctions to extract data related to spatial annotations. |
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Obtain a SpatialAnnotation object |
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Obtain list of SpatialAnnotation objects |
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Obtain area of spatial annotation |
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Obtain barcodes by spatial annotations |
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Obtain center of a spatial annotation |
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Obtain center data point |
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Obtain IDs of spatial annotations |
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Obtain the outline of a spatial annotation |
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Obtain spatial annotations range |
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Obtain the outline of a spatial anontation |
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Obtain spatial annotation tags |
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Spatial TrajectoriesFunctions to extract data related to spatial trajectories. |
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Obtain trajectory projection |
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Obtain SpatialTrajectory objects |
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Obtain trajectory IDs |
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Obtain length of spatial trajectory |
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Obtain trajectory course |
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Obtain trajectory width |
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Tissue, Tissue Outline & Spatial MeasuresFunctions to extract tissue related data. |
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Obtain capture area |
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Obtain center to center distance |
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Obtain default unit |
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Obtain spatial method |
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Obtain tissue area size |
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Obtain tissue outline centroid |
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Obtain the outline of tissue sections |
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Obtain the names of tissue sections |
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MiscellaneousFunctions to extract miscellaneous types of data. |
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Obtain barcodes |
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Obtain default argument inputs |
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Obtain object logfile data.frame |
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Obtain platform details |
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Obtain platform name |
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Obtain name of SPATA2 object |
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Obtain scale factors |
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Obtain a data.frame of observations |
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Obtain SPATA2 object directory |
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Obtain SpatialData object |
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Obtain variable names of the SPATA2 object |
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Remove ContentRemove miscellaneous kinds of data from a SPATA2 object. |
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Register or remove images |
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Remove meta features |
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Remove molecules from the SPATA2 object |
Remove observations |
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Remove a processed matrix |
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Remove spatial annotations |
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Remove spatial outliers |
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Remove spatial trajectories |
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Remove data points from tissue fragments |
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Management of Grouping VariablesFunctions to change grouping variables. |
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Lump groups together |
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Dissolve groups in a SPATA2 object |
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Rename cluster/group names |
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Relevel groups of grouping variable |
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Spatial Annotation HandlingFunctions to create and work with spatial annotations. |
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Create Spatial Annotations |
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Add a spatial annotation with data input |
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Create spatial annotations from a list of barcodes |
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Create spatial annotations from a group of data points |
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Create spatial annotations based on histo-morphological features |
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Create spatial annotations based on numeric values |
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Manipulate Spatial Annotations |
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Center the borders of a spatial annotation |
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Expand the outline of spatial annotations |
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Merge spatial annotations |
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Rename a spatial annotation |
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Rotate the outline of a spatial annotation |
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Shift the borders of a spatial annotation |
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Smooth the border of a spatial annotation |
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Tag spatial annotations |
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Use Spatial Annotations |
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Spatial annotation and barcode intersection |
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Convert spatial annotation to grouping variable |
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Image handling and Image-Coordinate AlignmentFunctions to work with and ensure alignment between images and coordinates of observations. |
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Mirror invert image and coordinates |
Load image slot content |
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Obtain name of reference iamge |
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Register or remove images |
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Resize image |
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Reset image transformations |
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Rotate image and coordinates |
Rotate the outline of a spatial annotation |
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Unload image slot content |
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Write image to disk |
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Join InformationThese 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. |
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Join barcodes with additional variables |
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Join data with variables |
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Implemented AlgorithmsThese functions perform calculations that might take some time. The results are stored inside the SPATA2 object. |
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Compute capture area |
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Compute CNV by chromosome arm |
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Compute count percentage |
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Compute meta features |
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Compute pixel scale factor |
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Clustering with BayesSpace |
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Identify large-scale chromosomal copy number variations |
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Differential expression analysis (DEA) |
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Compute gene set enrichment |
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Clustering with Kmeans |
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Clustering with nearest neighbor search |
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Run Principal Component Analysis |
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Identify spatially significant features with SPARKX |
Clustering with Seurat |
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Run t-Stochastic Neighbour Embedding |
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Run Uniform Manifold Approximation and Projection |
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Compute scale factor of two images |
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Tissue Outline & Tissue SectionsFunctions that incorporate the spatial dimensions and outline of the tissue using data points or images as information. |
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Distance to edge of tissue section |
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Identify pixel content |
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Identify tissue outline |
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Identify spatial outliers |
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Merge tissue sections |
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Integrate tissue outline in spatial annotation |
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Rename cluster/group names |
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Use specified variable for tissue outline |
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Tissue section belonging of spatial annotations |
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Miscellaneous Spatial Functions |
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Add tissue section variable to coordinate data.frame |
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Add edge variable to coordinate data.frame |
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Add grid variable to coordinate data.rame |
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Buffer area |
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Identify observations inside a polygon |
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Include spatial extent of tissue sections in analysis |
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Test polygon intersection |
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Map observations to tissue sections |
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Merge polygons |
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Spatial Gradient ScreeningFunctions around Spatial Trajectory Screening and Image Annotation Screening. |
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Low level implementation of the spatial gradient screening algorithm |
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The Spatial Annotation Screening algorithm |
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The Spatial Trajectory Screening algorithm |
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Obtain spatial trajectory screening data.frame |
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Obtain spatial annotation screening data.frame |
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Plot SAS barplot |
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Plot SAS densityplot |
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Plot SAS heatmap |
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Plot SAS lineplot |
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Plot SAS rideplot |
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Spatial MeasuresFunctions to work with spatial measures in SI units. |
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Test area or distance input |
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Transform distance and area values |
Distance transformation |
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Extract distance units |
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Extract distance value |
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Test area input |
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Test distance input |
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Test unit of area input |
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Test unit of length input |
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S4 ClassesThe S4 classes SPATA2 uses to abstract concepts of spatial multi-omic experiments. |
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PlatformsVariables that have been defined as objects of class |
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MERFISH Spatial Method |
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VisiumSmall Spatial Method |
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VisiumHD Spatial Method |
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VisiumLarge Spatial Method |
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SlideSeqV1 Spatial Method |
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Xenium Spatial Method |
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Visualization |
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Copy Number Variation |
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Plot CNV Heatmap |
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Plot CNV Lineplot |
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DEA & GSEAVisualize the results of differential expression analysis and gene set enrichment analysis. |
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Plot DEA results via dot plots |
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Plot DEA results via heatmaps |
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Plot DEA results via volcano plots |
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Plot GSEA results via dot plots |
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Dimensional ReductionVisualize the barcode spots in a reduced dimension fashion. |
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Plot dimensional reduction |
Plot PCA Elbow Plot |
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Plot PCA Variation |
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ggpLayer and other gg objectsAdd ggroto objects to ggplot2 plots. |
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Initiate ggplot2 layering |
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Display clean axes |
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Display axes with SI units of length |
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Add capture area to surface plot |
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Add group specific color spectrum |
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Add SAS expression estimates |
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Fix ggplot frame |
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Set plot limits |
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Add a grid to VisiumHD surface plots |
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Add group outline |
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Add SAS screening horizon |
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Add histology image |
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Add the observations to the surface plot |
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Add a rectangular to the plot |
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Add a scale bar in SI units |
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Add SAS screening direction |
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Add outline of spatial annotations |
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Add pointer towards spatial annotations |
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Add a rectangular around an spatial annotation |
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Add spatial trajectories |
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Add coordinates theme |
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Add a hull outlining the tissue |
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Add the screening frame of a spatial trajectory |
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Set plot limits manually |
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ggplot2 themes |
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ggplot2 basic manipulation |
geoms |
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Points (fixed size ~ window ratio) |
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Segments (fixed size ~ window ratio) |
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Text (fixed size ~ window ratio) |
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Image |
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Plot histology image |
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Plot histology images |
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Plot image with R base plotting |
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Plot pixel content |
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MiscellaneousVisualize a variety of aspects. |
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Plot Bayes Space logliks |
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Plot numeric variables as a scatterplot |
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Show color palettes and spectra |
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Show spatial gradient screening models |
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Spatial Gradient |
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Plot expression as a function of distance to a spatial references |
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Plot spatial annotations |
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Plot spatial trajectories |
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Plot SAS barplot |
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Plot SAS densityplot |
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Plot SAS heatmap |
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Plot SAS lineplot |
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Plot SAS rideplot |
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Plot STS barplot |
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Plot STS heatmap |
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Plot STS line- and ridgeplot |
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Statistics |
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Plot distribution of discrete variables |
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Plot numeric distribution and statistical tests |
Plot mosaic plot |
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Plot riverplots |
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Plot distribution of variables interactively |
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Surface Plots & 2D data |
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Plot the surface of the sample |
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Plot surface with R base plotting |
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Plot several surface plots colored by numeric variables |
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Plot screening area of SAS set up |
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Plot single cells on surface |
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Plot molecules in 2D space |
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Miscellaneous Functions |
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The current version of SPATA2 |
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Information about deprecated aspects |
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Check for outliers in a numeric vector |
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General test for SPATA2 object |
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Convert Image to Binary with Flexible Thresholding |
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Generate model-based ascending or descending sequence |
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Model a peaking pattern |
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The observational unit |
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Platform dependent input recommendations |
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Read coordinate data.frames |
Read Matrix from Folder |
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Transform coordinates |
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Transform image |
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Map aggregated to pre-aggregated barcodes |