Man pages for theMILOlab/SPATA2
A Toolbox for Spatial Expression Analysis
| activateAssay | Default assay name |
| activateGrouping | Default grouping |
| activateImage | Default image name |
| activateMatrix | Default matrix name |
| addAutoencoderSetUp | Add the set up of a neural network |
| add_dbscan_variable | Add tissue section variable to coordinate data.frame |
| add_edge_variable | Add edge variable to coordinate data.frame |
| addExpressionMatrix | Deprecated |
| addFeatures | Add meta variables for observations |
| add_grid_variable | Add grid variable to coordinate data.rame |
| addHistoImage | Add object of class 'HistoImage' |
| addImageAnnotation | Deprecated |
| addInnerBorder | Add holes to spatial annotations |
| addMetaDataMol | Add meta variables for molecular data |
| addMetaDataObs | Add meta variables for observations |
| add_models | Add models to a data.frame |
| addMoleculeCoordinates | Add molecule coordinates |
| add_noise_to_model | Add Noise to a Model |
| addPointsBase | Add points to base surface plot |
| addPolygonBase | Add polygons to a base plot |
| addProcessedMatrix | Add a processed matrix |
| addSegmentationVariable | Add Segmentation Variable |
| addSignature | Add molecular signature |
| addSpatialAnnotation | Add a spatial annotation with data input |
| addSpatialTrajectory | Add a spatial trajectory with data input |
| addSpCorCluster | Add cluster results of spatial correlation results |
| addTissueOutlineBase | Add polygons to a base plot |
| addVarToCoords | Add variable to coordinates data.frame |
| add_wh | Add width and height or x and y |
| adjustDefaultInstructions | Deprecated |
| adjustGeneSetList | Adjust Gene Set List |
| alignImage | Align histology images |
| all_color_palettes | Color palette names |
| allColorpalettes | Valid colorpanels & -spectra |
| append_polygon_df | Append polygon df |
| are_all_area_or_dist | Test area or distance input |
| argument_dummy | Argument dummy |
| arrange_as_polygon | Arrange observations as polygon |
| asGiotto | Transform SPATA2 object to Giotto object |
| asMolecularAssay | Transform miscellaneous objects to MolecularAssay objects |
| asSeurat | Transform SPATA2 object to Seurat object |
| asSingleCellExperiment | Transform SPATA2 object to SingleCellExperiment object |
| asSPATA2 | Transform miscellaneous objects to SPATA2 objects |
| as_SPATA2_dist | Distance transformation |
| asSpatialTrajectory | Transform to 'SpatialTrajectory' |
| asSummarizedExperiment | Transform SPATA2 object to SummarizedExperiment object |
| as_unit | Transform distance and area values |
| attachUnit | Attach unit to distance |
| average_genes | average_genes |
| background_white | Remove Background and Set it to White |
| barcodesToSpatialAnnotation | Create spatial annotations from a list of barcodes |
| binwidth_dummy | binwidth |
| buffer_area | Buffer area |
| cds_dummy | Title |
| centerSpatialAnnotation | Center the borders of a spatial annotation |
| centerTissueOutline | Center tissue |
| check_assign | Check assign input |
| check_availability | Gives feedback if object was not found |
| check_color_to | Check color to |
| check_coordinate_variables | Check coordinate variables |
| check_coords_df | Check coords data.frame |
| check_dea_df | Check de data.frame |
| check_display | Check display input |
| check_feature_df | Check feature data.frame |
| check_features | Check feature variables input |
| check_genes | Check gene input |
| check_gene_sets | Check gene set input |
| check_method | Check method input |
| check_monocle_input | Check monocle input |
| check_monocle_packages | Makes sure that both packages are installed |
| check_paths | Check candidate paths |
| check_pattern | Check pattern input |
| checkpoint | Shiny feedback messages |
| check_pt | Check pt input |
| check_sample | Check sample input |
| check_saving | Check saving input |
| check_segment | Check segment name |
| check_smooth | Check smooth input |
| check_spata_df | Check coordinate data.frame |
| check_stdf | Check summarized trajectory data.frame |
| check_summarized_trajectory_df | Check stdf-input |
| check_to | Gives feedback about input validity |
| check_trajectory | Check trajectory name input |
| check_trajectory_binwidth | Check trajectory binwdith input |
| check_uniform_genes | Check uniform genes input |
| check_variables | Check variables |
| close_area_df | Close area encircling |
| clrp | clrp |
| clusterSpCorResults | Cluster genes according to their expression profile |
| cnv_ref | A list of reference data for copy number variation analysis... |
| cnv_regions_df | A data.frame necessary for cnv-analysis. Contains information... |
| color_vector | Get vector of colors |
| compute_angle_between_two_points | Compute angle between two points |
| computeCaptureArea | Compute capture area |
| computeChromosomalInstability | Compute chromosomal damage |
| computeCnvByChrArm | Compute CNV by chromosome arm |
| computeCountPercentage | Compute count percentage |
| compute_distance | Compute the distance between to points |
| compute_expression_estimates | Compute |
| compute_img_scale_fct | Compute scale factor of two images |
| computeMetaFeatures | Compute meta features |
| computePixelScaleFactor | Compute pixel scale factor |
| concept_active | Active / Inactive |
| concept_area_measure | Area measures |
| concept_distance_measure | Distance measures |
| concept_images | Images |
| concept_logfile | Logfile (Logfile Data) |
| concept_molecular_modalities | Molecular Modalities |
| concept_molecular_signatures | Molecular Signatures |
| concept_observations | Observations (Data points) |
| concept_scale_factors | Scale Factors |
| concept_spatial_annotation | Spatial Annotations |
| concept_spatial_trajectory | Spatial Gradient Screening |
| concept_tissue_outline | Tissue Outline |
| concept_variables | Variables (Features) |
| containsAssay | Check availability of an assay |
| containsCaptureArea | Check availability of capture area |
| containsCCD | Check availability of center to center distance |
| containsCells | Check availability of cells |
| containsCNV | Check availability CNV results |
| containsHistoImages | Check availability of image containers |
| containsHistologyImaging | Deprecated |
| 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 |
| containsPseudoImage | Check if the object contains only a pseudo image |
| 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 |
| containsVersion | Checks availability of slot @version |
| countImageAnnotationTags | Count image annotation tags |
| createGroupAnnotations | Create spatial annotations from a group of data points |
| createHistoImage | Create an object of class 'HistoImage' |
| createImageAnnotations | Create spatial annotations based on histo-morphological... |
| create_model_df | Create model data.frame |
| createMolecularAssay | Create and add an object of class 'MolecularAssay' |
| createNumericAnnotations | Create spatial annotations based on numeric values |
| createSegmentation | Deprecated |
| createSpatialData | 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 |
| createTrajectories | Deprecated |
| createTrajectoryManually | Deprecated |
| crop_image | Crop image |
| cropSpataObject | Crop SPATA2 object |
| currentSpata2Version | The current version of SPATA2 |
| data_counts-class | The 'data_counts'- Class |
| defaultGeomObs | Default observations geometry |
| default_instructions-class | default instructions |
| deprecatedInfo | Information about deprecated aspects |
| dim_red-class | The 'dim_red'- Class |
| dissolveGroups | Dissolve groups in a SPATA2 object |
| distToEdge | Distance to edge of tissue section |
| downloadFromPublication | Download data from publications |
| downloadSpataObject | Download a SPATA2 object |
| downloadSpataObjects | Download and save several SPATA2 objects |
| dropped_df_dummy | dropped_df |
| example_data | Data required for reproducible examples in SPATA2 tutorials. |
| exchangeImage | Deprecated |
| expandSpatialAnnotation | Expand the outline of spatial annotations |
| export | dummy |
| extract_row_col_vars_visiumHD | Extract Row and Column Variables for VisiumHD Barcodes |
| extract_unit | Extract distance units |
| extract_value | Extract distance value |
| extract_var_names | Extract var names from filter expression |
| filterDeaDf | Postprocess DEA results |
| filterSpataObject | Subset SPATA2 object with logical expressions |
| find_neighbors_visiumHD | Find Neighbors in VisiumHD Data |
| find_path | Find a Resource Path |
| findSDEGS | Spatial Differential Gene Expression |
| flexible_call_dummy | flexible_call_dummy |
| flipAll | Mirror invert image and coordinates |
| flipCoords | Deprecated |
| flip_coords_df | Flip coordinate variables |
| gene_pos_df | A data.frame necessary for cnv-analysis. Contains information... |
| gene_set_path | gene_set_path |
| geom_point_fixed | Points (fixed size ~ window ratio) |
| GeomPointFixed | GeomPointFixed |
| geom_segment_fixed | Segments (fixed size ~ window ratio) |
| GeomSegmentFixed | GeomSegmentFixed |
| geom_text_fixed | Text (fixed size ~ window ratio) |
| GeomTextFixed | GeomTextFixed |
| getActive | Obtain name of active content |
| getActiveExpressionMatrixName | Deprecated |
| getActiveMatrixName | Deprecated |
| getAssay | Obtain molecular assay |
| getAssayModalities | Obtain assay names/modalites |
| getAutoencoderAssessment | Obtain information about the optimal neural network set up |
| getAutoencoderSetUp | Obtain information on neural network |
| getBackgroundColor | Obtain background color |
| getBarcodes | Obtain barcodes |
| getBarcodesInPolygon | Obtain barcodes in polygon |
| getBarcodeSpotDistance | Deprecated |
| getBarcodeSpotDistances | Obtain distances between barcodes |
| getCaptureArea | Obtain capture area |
| getCCD | Obtain center to center distance |
| getChrRegionsDf | Obtain chromosome information |
| getCnvFeatureNames | Obtain features names under which cnv-analysis results are... |
| getCnvGenesDf | Obtain CNV results by gene |
| getCnvResults | Obtain CNV results |
| getCoordsCenter | Obtain coordinate center |
| getCoordsDf | Obtain coordinates |
| getCoordsDfSA | Relate points to spatial annotations |
| getCoordsMtr | Obtain coordinates matrix |
| getCoordsRange | Obtain coordinate range |
| getCountMatrix | Obtain raw counts |
| getDeaLfcName | Obtain LFC name |
| getDeaResultsDf | Obtain DEA results |
| getDefaultGrouping | Deprecated |
| getDefaultInstructions | Obtain default argument inputs |
| getDefaultUnit | Obtain default unit |
| getDimRedDf | Obtain dim red data.frame |
| getExpressionMatrix | Deprecated |
| getExpressionMatrixNames | Deprecated |
| getFeatureDf | Deprecated |
| getFromSeurat | Safe extraction |
| getGeneDistMtr | Obtain distance measurements of spatially correlated genes |
| getGeneMetaData | Deprecated |
| getGenePosDf | Obtain gene CNV information |
| getGeneSetDf | Obtain gene sets |
| getGridVisiumHD | Obtain grid information |
| getGroupingOptions | Obtain variable names that group data points |
| getGroupNames | Obtain group names a grouping variable contains |
| getGseaDf | Obtain enrichment data.frame |
| getGseaResults | Obtain enrichment results |
| getHistoImage | Obtain HistoImage object |
| getImage | Obtain image |
| getImageAnnotationAreaDf | Deprecated |
| getImageAnnotationCenter | Deprecated |
| getImageAnnotationIds | Deprecated |
| getImageAnnotationTags | Deprecated |
| getImageCenter | Obtain image center |
| getImageDf | Obtain image as a data.frame |
| getImageDims | Obtain image dimensions/ranges |
| getImageDir | Obtain directory to image |
| getImageDirDefault | Deprecated |
| getImageDirHighres | Deprecated |
| getImageDirLowres | Deprecated |
| getImageNames | Obtain names of registered images |
| getImageRaster | Obtain image raster-(information) |
| getImageSectionsByBarcode | Obtain image sections by barcode |
| getImageTransformations | Obtain image transformation instructions |
| getImgAnnArea | Deprecated |
| getImgAnnBorderDf | Deprecated |
| getImgAnnCenter | Deprecated |
| getImgAnnCenters | Deprecated |
| getImgAnnIds | Deprecated |
| getImgAnnOutlineDf | Deprecated |
| getImgAnnRange | Deprecated |
| getImgAnnTags | Deprecated |
| getLogfileDf | Obtain object logfile data.frame |
| getMatrix | Obtain a data matrix |
| getMatrixNames | Obtain matrix names |
| getMetaDf | Obtain meta data.frame for observations |
| getMetaNames | Obtain metadata column names |
| getMetaVarDf | Obtain molecular meta data.frame |
| getMethodSpecifics | Obtain platform details |
| getModality | Obatin molecular modality |
| getMoleculeCoordinates | Obtain molecule coordinates |
| getMolecules | Obtain molecule names |
| getMoleculeTypeList | Obtain a list of molecules |
| get_names_dummy | get_names |
| getPixelDf | Obtain pixel data.frame |
| getPixelScaleFactor | Obtain scale factor for pixel to SI conversion |
| getPlatform | Obtain platform name |
| getProcessedMatrix | Obtain processed data matrix |
| getProcessedMatrixNames | Obtain names of processed matrices |
| getProjectionDf | Obtain trajectory projection |
| getPrResults | Obtain pattern recognition results |
| getResultsDf | Deprecated |
| getResultsVec | Deprecated |
| getSampleAreaSize | Deprecated |
| getSampleName | Obtain name of SPATA2 object |
| getSasDf | Obtain spatial annotation screening data.frame |
| getScaleFactor | Obtain scale factors |
| getSegmentationNames | Deprecated |
| getSgsResultsDf | Obtain spatial gradient screening results |
| getSgsResultsVec | Obtain spatial gradient screening results |
| getSignature | Obtain molecular signature |
| getSignatureList | Obtain molecular signatures |
| getSignatureNames | Obtain molecular signature names |
| getSignatureOverview | Overview about the current signature collection |
| getSignatureTypeList | Obtain a list of signatures |
| getSmrdResultsDf | Deprecated |
| getSpataDf | Obtain a data.frame of observations |
| getSpataDir | Obtain SPATA2 object directory |
| getSpatAnnArea | Obtain area of spatial annotation |
| getSpatAnnBarcodes | Obtain barcodes by spatial annotations |
| getSpatAnnCenter | 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 |
| getSpatialAnnotation | Obtain a SpatialAnnotation object |
| getSpatialAnnotations | Obtain list of SpatialAnnotation objects |
| getSpatialData | Obtain SpatialData object |
| getSpatialMethod | Obtain spatial method |
| getSpatialTrajectory | Obtain SpatialTrajectory objects |
| getSpatialTrajectoryIds | Obtain trajectory IDs |
| getSpatSegmVarNames | Obtain segmentation variable names |
| getSpCorCluster | Obtain cluster results based on spatial correlation analysis |
| getSpCorResults | Obtain spatial correlation results |
| getSpotSize | Obtain spot size |
| getStsDf | Obtain spatial trajectory screening data.frame |
| getTissueArea | Obtain tissue area size |
| getTissueOutlineCentroid | Obtain tissue outline centroid |
| getTissueOutlineDf | Obtain the outline of tissue sections |
| getTissueSections | Obtain the names of tissue sections |
| getTrajectory | Deprecated |
| getTrajectoryDf | Deprecated |
| getTrajectoryIds | Deprecated |
| getTrajectoryLength | Obtain length of spatial trajectory |
| getTrajectoryNames | Deprecated |
| getTrajectoryObject | Deprecated |
| getTrajectoryScreeningDf | Deprecated |
| getTrajectorySegmentDf | Obtain trajectory course |
| getTrajectoryWidth | Obtain trajectory width |
| getVariableMolecules | Obtain molecules of high variability |
| getVariableNames | Obtain variable names of the SPATA2 object |
| getVarTypeList | Get variable type list |
| getWindowSize | Obtain window size of padded image |
| 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 |
| ggpLayer_dummy | ggpLayer |
| ggpLayerEncirclingGroups | Deprecated |
| ggpLayerEncirclingSAS | Deprecated |
| ggpLayerExprEstimatesSAS | Add SAS expression estimates |
| ggpLayerFrame | Fix ggplot frame |
| ggpLayerFrameByCoords | Set plot limits |
| ggpLayerGridVisiumHD | Add a grid to VisiumHD surface plots |
| ggpLayerGroupOutline | Add group outline |
| ggpLayerHorizonSAS | Add SAS screening horizon |
| ggpLayerImage | Add histology image |
| ggpLayerImageAnnotation | Deprecated |
| ggpLayerImgAnnBorder | Deprecated |
| ggpLayerPoints | Add the observations to the surface plot |
| ggpLayerRect | Add a rectangular to the plot |
| ggpLayerSampleMask | Deprecated |
| 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 |
| ggpLayerTrajectories | Deprecated |
| ggpLayerTrajectoryFrame | Add the screening frame of a spatial trajectory |
| ggpLayerZoom | Set plot limits manually |
| ggplot_dummy | ggplot |
| ggplot_family | ggplot_family |
| GroupAnnotation-class | The 'GroupAnnotation' - Class |
| HistoImage-class | The 'HistoImage' - Class |
| HistoImaging-class | The 'HistoImaging' - Class |
| HistologyImage-class | The 'HistologyImage' - Class |
| HistologyImaging-class | The 'HistologyImaging' - Class |
| hlpr_vector_projection | Perform vector projection |
| identifyBackgroundColor | Identifies the background color |
| identify_obs_in_polygon | Identify observations inside a polygon |
| identifyPixelContent | Identify pixel content |
| identifySpatialOutliers | Identify spatial outliers |
| identifyTissueOutline | Identify tissue outline |
| identifyTissueSections | Deprecated |
| identifyVariableMolecules | Identify molecules of high variability |
| idSA | Quick access to IDs |
| ImageAnnotation-class | The 'ImageAnnotation' - Class |
| image_dummy | image_dummy |
| include_tissue_outline | Include spatial extent of tissue sections in analysis |
| increase_n_data_points | Increase the Number of Data Points in a Coordinate Data Frame |
| increase_polygon_vertices | Increase the Number of Vertices in a Polygon |
| 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 |
| interpolate_points_along_path | Interpolate points along path |
| intersect_polygons | Test polygon intersection |
| is_area | Test area input |
| isDirVisium | Directory tests |
| is_dist | Test distance input |
| is_inside_plg | Check if a Point is Inside a Polygon |
| is_outlier | Check for outliers in a numeric vector |
| isSPATA2 | General test for SPATA2 object |
| is_unit_area | Test unit of area input |
| is_unit_dist | Test unit of length input |
| joinWith | Join barcodes with additional variables |
| joinWithPca | Join barcodes with additional variables |
| joinWithVariables | Join data with variables |
| lastImageAnnotation | Deprecated |
| legendBottom | ggplot2 basic manipulation |
| loadExampleObject | Load example SPATA2 object |
| loadImage | Load image slot content |
| loadImageLowres | Deprecated |
| loadSpataObject | Load SPATA2 object |
| make_binary_image | Convert Image to Binary with Flexible Thresholding |
| makeContent.resizingSegmentsGrob | Make content for segments grob |
| makeContent.resizingTextGrob | Make content for text grob |
| make_orthogonal_segment | Compute an orthogonal vector |
| make_orthogonal_segments | Make orthogonal segments |
| mapSpatialAnnotationTags | Spatial annotation and barcode intersection |
| map_to_tissue_section | Map observations to tissue sections |
| matrix_dummy | matrix_dummy |
| MERFISH | MERFISH Spatial Method |
| mergeGroups | Lump groups together |
| merge_intersecting_polygons | Merge polygons |
| mergeSpatialAnnotations | Merge spatial annotations |
| mergeTissueSections | Merge tissue sections |
| mergeWithTissueOutline | Integrate tissue outline in spatial annotation |
| method_hclust | method_hclust |
| model_ascending | Generate model-based ascending or descending sequence |
| model_peak | Model a peaking pattern |
| moduleAddGeneSetsServer | Server of the add gene sets module |
| moduleAddGeneSetsUI | UI of the add gene sets module |
| moduleSurfacePlotServer | Server of the surface plot module |
| moduleSurfacePlotUI | UI of the surface plot module |
| MolecularAssay-class | The 'MolecularAssay' - Class |
| nImages | Number of images |
| nMolecules | Number of molecules |
| nObs | Number of observations |
| normalize | Normalize variable |
| normalizeCounts | Normalize raw counts |
| nSpatialAnnotations | Number of spatial annotations |
| nSpatialTrajectories | Number of spatial trajectories |
| NumericAnnotation-class | The 'NumericAnnotation' - Class |
| object_dummy | object |
| obsUnit | The observational unit |
| pb_dummy | pb |
| plotAutoencoderAssessment | Plot total variance of different neural networks |
| plotAutoencoderResults | Plot scaled vs. denoised expression |
| plotBarchart | Plot distribution of discrete variables |
| plotBoxplot | Plot numeric distribution and statistical tests |
| plotCnvHeatmap | Plot CNV Heatmap |
| plotCnvLineplot | Plot CNV Lineplot |
| plotCnvResults | Deprecated |
| plotDeaDotPlot | Plot DEA results via dot plots |
| plotDeaHeatmap | Plot DEA results via heatmaps |
| plotDeaVolcano | Plot DEA results via volcano plots |
| plotDendrogram | dummy |
| plotExprVsDistSA | Plot expression as a function of distance to a spatial... |
| plotGeneDendrogram | Visualize clustering results |
| plotGseaDotPlot | Plot GSEA results via dot plots |
| plotImage | Plot histology image |
| plotImageAnnotations | Deprecated |
| plotImageBase | Plot image with R base plotting |
| plotImageMask | Plot pixel content |
| plotImages | Plot histology images |
| plotLoglik | Plot Bayes Space logliks |
| plot_model_comparison_dotplot | Plot Model Comparison Dotplot |
| plotMolecules2D | Plot molecules in 2D space |
| plotMosaicplot | Plot mosaic plot |
| plotOverview | Plot overview of S4 objects |
| plotPcaElbow | Plot PCA Elbow Plot |
| plotPcaVariation | Plot PCA Variation |
| plotRiverplot | Plot riverplots |
| plotSasBarplot | Plot SAS barplot |
| plotSasDensityplot | Plot SAS densityplot |
| plotSasHeatmap | Plot SAS heatmap |
| plotSasLineplot | Plot SAS lineplot |
| plotSasRidgeplot | Plot SAS rideplot |
| plotScatterplot | Plot numeric variables as a scatterplot |
| plot_screening_evaluation | Helper |
| plotSpatialAnnotations | Plot spatial annotations |
| plotSpatialTrajectories | Plot spatial trajectories |
| plotStatisticsInteractive | Plot distribution of variables interactively |
| plotStsBarplot | Plot STS barplot |
| plotStsHeatmap | Plot STS heatmap |
| plotStsLineplot | Plot STS line- and ridgeplot |
| plotSurface | Plot the surface of the sample |
| plotSurfaceBase | Plot surface with R base plotting |
| plotSurfaceComparison | Plot several surface plots colored by numeric variables |
| plotSurfaceQuantiles | Deprecated |
| plotSurfaceSAS | Plot screening area of SAS set up |
| plotSurfaceSC | Plot single cells on surface |
| plotTrajectoryBarplot | Deprecated |
| plotTrajectoryHeatmap | Deprecated |
| plotTrajectoryLineplot | Deprecated |
| plot_type_dummy | plot_type |
| plotUmap | Plot dimensional reduction |
| plotVolcano | Compare evaluation of spatially opposing fits |
| polygon_inside_polygon | Check polygon containment and intersection |
| prepare_coords_df_visium_hd | Prepare coordinates data.frame for decreasing resolution |
| printAutoencoderSummary | Print autoencoder summary |
| printDefaultInstructions | Print current default settings |
| print_family | |
| printGeneSetOverview | Deprecated |
| process_expand_input | Process expand input |
| processImage | Run image processing pipeline |
| process_ranges | Process input ranges |
| project_on_trajectory | Project barcode spots on a trajectory |
| project_on_vector | Perform vector projection |
| read_coords | Read coordinate data.frames |
| read_matrix_from_folder | Read Matrix from Folder |
| recSgsRes | Platform dependent input recommendations |
| reduce_coords_df_visium_hd | Reduce resolution coordinates data.frame |
| reduceResolutionVisiumHD | Reduce resolution for Visium HD data |
| reduceSpataObject | Reduce SPATA2 object |
| reduce_vec | Reduces vector length |
| refImage | Obtain name of reference iamge |
| regexes | Regular Expressions for Data Validation and Parsing |
| registerImage | Register or remove images |
| relateToSpatialAnnotation | Deprecated |
| relevelGroups | Relevel groups of grouping variable |
| removeMetaFeatures | Remove meta features |
| removeMolecules | Remove molecules from the SPATA2 object |
| removeObs | 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 |
| renameGroups | 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. |
| resetImageJustification | Deprecated |
| resetImageTransformations | Reset image transformations |
| resizeImage | Resize image |
| resizingSegmentsGrob | Used for GeomSegmentFixed |
| resizingTextGrob | Used for GeomTextScaled |
| rotateAll | Rotate image and coordinates |
| rotate_coords_df | Rotate coordinate variables pairs |
| rotateSpatialAnnotation | Rotate the outline of a spatial annotation |
| runAutoencoderAssessment | Assessment of Neural Network Set Up |
| runAutoencoderDenoising | Denoise expression matrix |
| runBayesSpaceClustering | Clustering with BayesSpace |
| runCIN | Compute chromosomal instability |
| runCNV | Identify large-scale chromosomal copy number variations |
| runDEA | Differential expression analysis (DEA) |
| runGSEA | Compute gene set enrichment |
| runKmeansClustering | Clustering with Kmeans |
| runNearestNeighborClustering | Clustering with nearest neighbor search |
| runPca | Run Principal Component Analysis |
| runSDEA | Run spatial differential expression analysis |
| runSeuratClustering | Clustering with Seurat |
| runSparkx | Identify spatially significant features with SPARKX |
| runSpatialCorrelationAnalysis | Initiate gene clustering analysis based on spatial patterns |
| runSPROD | De-noise expression data based on position and image... |
| runTsne | Run t-Stochastic Neighbour Embedding |
| runUmap | Run Uniform Manifold Approximation and Projection |
| sample_name | sample_name |
| saveSpataObject | Save SPATA2 object with a default directory |
| scale_color_add_on | ggplot2 - color add on |
| scale_coords_df | Scale coordinate variable pairs |
| SDEGS-class | The 'SDEGS'-class |
| section_dummy | Section dummy |
| segments_to_vertices | Transform segments to vertices |
| setActiveExpressionMatrix | Deprecated |
| setActiveMatrix | Deprecated |
| setAssay | Set MolecularAssay objects |
| setAutoencoderAssessment | Set results of autoencoder assessment |
| setBarcodes | Set barcodes |
| setCaptureArea | Set capture area |
| setCCD | Set center to center distance |
| setCnvResults | Set CNV results |
| setCoordsDf | Set the coordinates |
| setCountMatrix | Set data matrices |
| setDefault | Set object specific default |
| setDefaultInstructions | Set default instructions |
| setDenoisedMatrix | Deprecated |
| set_dummy | set |
| setHistoImage | Set HistoImage object |
| setImage | Deprecated |
| setImageAnnotation | Deprecated |
| setImageDir | Set image directory |
| setImageTransformations | Set image transformation instructions |
| setLogfileDf | Set logfile data.frame |
| setMetaDf | Set meta data.frame |
| setMetaVarDf | Set molecular meta data.frame |
| setPcaDf | Set dimensional reductions data.frames |
| setPrResults | Set results of pattern recognition methods |
| setScaleFactor | Set scale factors |
| setSpataDir | Set SPATA2 directory |
| setSpatialAnnotation | Set SpatialAnnotation objects |
| setSpatialData | Set SpatialData object |
| setSpatialMethod | Set SpatialMethod object |
| setSpatialMethodInfo | Set information of SpatialMethod object |
| setSpatialMethodSlot | Set slot content of SpatialMethod object |
| setSpatialTrajectory | Set SpatialTrajectory objects |
| setSpCorResults | Set results of spatial correlation analysis |
| setTrajectory | Deprecated |
| setUpMetaVar | Set up meta var slot |
| seurat_object_dummy | Title |
| shiftSpatialAnnotation | Shift the borders of a spatial annotation |
| shinyModuleZoomingServer | Shiny module _Zooming_ |
| showColors | Show color palettes and spectra |
| showModels | Show spatial gradient screening models |
| signatures | The default collection of frequently used signatures |
| simulate_expression_pattern_sas | Expression pattern simulation |
| simulate_random_gradients | Simulate Random Gradients |
| simulate_spatial_niches | Create a Spatial Niche in Coordinate Data Frame |
| SlideSeqV1 | SlideSeqV1 Spatial Method |
| smoothSpatialAnnotation | Smooth the border of a spatial annotation |
| smoothSpatially | Smooth numeric variables spatially |
| sort_into_components | Sort edges into components |
| SPATA2 | The 'SPATA2' - class |
| spata2-class | The 'spata2'- Class |
| SpatialAnnotation-class | The 'SpatialAnnotation' - Class |
| spatialAnnotationScreening | The Spatial Annotation Screening algorithm |
| SpatialAnnotationScreening-class | The 'SpatialAnnotationScreening' - Class |
| spatialAnnotationToGrouping | Convert spatial annotation to grouping variable |
| SpatialData-class | The 'SpatialData' - Class |
| spatial_gradient_screening | Low level implementation of the spatial gradient screening... |
| SpatialGradientScreening-class | The 'SpatialGradientScreening' - Class |
| SpatialMethod-class | The 'SpatialMethod' - Class |
| spatial_methods | List of Spatial Methods |
| spatial_trajectory-class | The 'spatial_trajectory'- Class |
| SpatialTrajectory-class | The 'SpatialTrajectory' - Class |
| spatialTrajectoryScreening | The Spatial Trajectory Screening algorithm |
| SpatialTrajectoryScreening-class | The 'SpatialTrajectoryScreening' - Class |
| splitSpataObject | Split SPATA2 object |
| subsetByBarcodes | Deprecated |
| subsetSpataObject | Subset SPATA2 object with barcodes |
| summarize_batch_reduce_visium_hd | Summarize and reduce Visium HD data by batch |
| summarize_formulas | List of summarizing formulas |
| tab_surface_plots_app | Surface plot tab - classic |
| tab_surface_plots_return | Surface plot tab - return |
| tagSpatialAnnotations | Tag spatial annotations |
| theme_lineplot_gradient | ggplot2 themes |
| Trajectory-class | The 'Trajectory' - Class |
| transfer_slot_content | Transfer S4 slot content |
| transform_area_si_to_pixel | Convert area in SI units to pixel |
| transform_coords | Transform coordinates |
| transform_dist_si_to_pixel | Convert from European Units of Length to pixels |
| transform_image | Transform image |
| transform_pixel_to_area_si | Converts from pixel to area in SI units |
| transform_pixel_to_dist_si | Convert from pixels to European units of length |
| transform_pixel_to_si | dummy |
| translate_shape_string | inspired from... |
| tutorial_hint_dummy | Title |
| unloadImage | Unload image slot content |
| unwindAggregation | Map aggregated to pre-aggregated barcodes |
| update_dummy | update |
| updateS4 | Update S4 objects |
| update_spata2v2_to_spata2v3 | doc |
| updateSpataObject | Update SPATA2 object |
| useVarForTissueOutline | Use specified variable for tissue outline |
| validActivationFunctions | Obtain valid argument inputs |
| validation | Validate object input |
| variable | variable |
| variable_num | variable_num |
| variables_num | variables_num |
| VisiumHD | VisiumHD Spatial Method |
| VisiumLarge | VisiumLarge Spatial Method |
| VisiumSmall | VisiumSmall Spatial Method |
| visiumSpotDistances | Calculate Distances Between Visium Spots |
| visium_spots | A list of a slot named _VisiumSmall_, which contains a list... |
| vselect | Select vector with tidyselect functions |
| whichTissueSection | Tissue section belonging of spatial annotations |
| writeImage | Write image to disk |
| Xenium | Xenium Spatial Method |
