Man pages for kueckelj/SPATA2
A Toolbox for Spatial Gene Expression Analysis
| across | across |
| addAutoencoderSetUp | Add the set up of a neural network |
| add_dbscan_variable | Add tissue section variable |
| addExpressionMatrix | Add an expression matrix |
| addFeatures | Add a new feature |
| addGeneFeatures | Add new gene features |
| addGeneMetaData | Add gene meta data to the object |
| addGeneSet | Add a new gene set |
| addImageDir | Add individual image directories |
| add_models | Add models to a data.frame |
| add_outline_variable | Add outline variable |
| addPointsBase | Add points to base surface plot |
| addSpCorCluster | Add cluster results of spatial correlation results |
| adjustDirectoryInstructions | Adjust default instructions |
| adjustGeneSetDf | Filter gene-set data.frame |
| alignImageAnnotation | Align image annotation |
| all_bcsp_distances | Obtain a all barcode-spots distances |
| 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' |
| asHistologyImage | Convert to class 'HistologyImage' |
| asHistologyImaging | Convert to class 'HistologyImaging' |
| asSeurat | Transform 'SPATA2' to 'Seurat' |
| asSingleCellExperiment | Transform to 'SingleCellExperiment' |
| asSPATA2 | Transform to 'spata2' object object |
| as_SPATA2_dist | Distance transformation |
| asSpatialTrajectory | Transform to 'SpatialTrajectory' |
| asSummarizedExperiment | Transform to 'SummarizedExperiment' |
| as_unit | Transform distance and area values |
| asVisiumV1 | Transform 'HistologyImage' to 'VisiumV1' |
| attachUnit | Attach unit to distance |
| average_genes | average_genes |
| barcodesToImageAnnotation | Create image annotations from a list of barcodes |
| bin_by_angle | Bin barcode-spots by angle |
| bin_by_expansion | Bin barcode-spots by area extension |
| binwidth_dummy | binwidth |
| buffer_area | Buffer area |
| cds_dummy | Title |
| check_all_barcodes | Check barcodes of all matrices and data.frames |
| check_assign | Check assign input |
| check_atdf | Check assessed trajectory data.frame |
| check_availability | Gives feedback if object was not found |
| check_color_to | Check color to |
| check_compiled_trajectory_df | Check compiled trajectory data.frame |
| check_coordinate_variables | Check coordinate variables |
| check_coords_df | Check coords data.frame |
| check_customized_trends | Check customized trend list |
| 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_object | Check spata object input |
| 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_slot_coordinates | Check spata slots |
| 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 |
| clustering | A list of data.frames that contain clustering variables for... |
| 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 |
| computeCnvByChrArm | Compute CNV by chromosome arm |
| compute_distance | Compute the distance between to points |
| computeGeneMetaData | Compute gene summary statistics |
| containsCNV | Check availability of miscellaneous content |
| containsHistologyImaging | Check availability of 'HistologyImaging' object |
| containsImage | Check availability of an image |
| containsPixelScaleFactor | Check availability of pixel scale factor |
| countImageAnnotationTags | Count image annotation tags |
| createHistologyImaging | Create object of class 'HistologyImaging' |
| createImageAnnotations | Add image annotations |
| create_model_df | Create model data.frame |
| createSegmentation | Deprecated in favor of 'createSpatialSegmentation()' |
| createSpatialSegmentation | Interactive sample segmentation |
| createSpatialTrajectories | Add spatial trajectories |
| cropSpataObject | Subset by x- and y-range |
| currentSpata2Version | The current version of 'SPATA2' |
| data_counts-class | data_counts object |
| dea | A nested list. First layer is named by the sample name.... |
| default_instructions-class | default instructions |
| deprecatedInfo | Information about deprecated aspects |
| dim_red-class | dim_red object |
| discardExpressionMatrix | Discard an expression matrix |
| discardFeatures | Discard features |
| discardGeneFeatures | Discard gene features |
| discardGenes | Discard genes |
| discardGeneSets | Discard gene sets |
| discardImageAnnotations | Discard image annotations |
| downloadPubExample | Download data from the publication |
| downloadRawData | Download raw Visium output |
| downloadSpataObject | Download 'spata2' objects |
| dropped_df_dummy | dropped_df |
| examineClusterResults | Examine clustering results |
| exchangeImage | Exchange image |
| export | dummy |
| extract_unit | Extract distance units |
| extract_value | Extract distance value |
| filterDeaDf | Postprocess de-analysis results |
| findMonocleClusters | Cluster sample via monocle3 |
| findNearestNeighbourClusters | Cluster sample via nearest neighbour analysis |
| findSeuratClusters | Cluster sample via Seurat |
| 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 |
| getActiveMatrixName | Obtain name of currently active data matrix |
| getAutoencoderAssessment | Obtain information about the optimal neural network set up |
| getAutoencoderSetUp | Obtain information on neural network |
| getBarcodes | Obtain specific barcodes |
| getBarcodesInPolygon | Obtain barcodes in polygon |
| getBarcodeSpotDistance | Obtain barcode spot distances |
| getBarcodeSpotDistances | Obtain distances between barcodes |
| 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 copy-number-variations results |
| getCoordsCenter | Obtain coordinate center |
| getCoordsDf | Obtain spatial coordinates |
| getCoordsRange | Obtain coordinate range |
| getDeaLfcName | Obtain LFC name |
| getDeaOverview | Obtain info on de-analysis storage |
| getDeaResultsDf | Obtain de-analysis results |
| getDefaultInstructions | Obtain default argument inputs |
| getDimRedDf | Obtain dim red data.frame |
| getExpressionMatrixNames | Obtain names of stored expression matrices |
| getFeatureDf | Obtain feature data |
| getFeatureNames | Obtain feature names |
| getFeatureValues | Obtain unique categorical feature values |
| getFeatureVariables | Obtain a feature variable |
| getFromSeurat | Safe extraction |
| getGeneCounts | Obtain total number of gene counts |
| getGeneDistMtr | Obtain distance measurements of spatially correlated genes |
| getGeneFeatureNames | Obtain feature names of the gene meta data |
| getGeneMetaData | Obtain gene meta data |
| getGenePosDf | Obtain gene information |
| getGenes | Obtain gene names |
| getGeneSetDf | Obtain gene set data.frame |
| getGeneSetOverview | Overview about the current gene sets |
| getGeneSets | Obtain gene set names |
| getGroupingOptions | Obtain variable names that group the barcode spots |
| getGroupNames | Obtain group names a grouping variable contains |
| getGseaDf | Obtain enrichment data.frame |
| getGseaResults | Obtain enrichment results |
| getIasBinAreas | Calculate IAS bin area |
| getIasDf | Obtain image annotation screening data.frame |
| getIasExpansion | Obtain expanded Image Annotation polygons |
| getImage | Obtain histology image |
| getImageAnnotation | Obtain object of class 'ImageAnnotation' |
| getImageAnnotations | Obtain list of 'ImageAnnotation'-objects |
| getImageCenter | Obtain image center |
| getImageDf | Obtain melted image |
| getImageDims | Obtain image dimensions/ranges |
| getImageDirLowres | Obtain image directories |
| getImageInfo | Obatain image information |
| getImageObject | Obtain object of class 'HistologyImage' |
| getImageOrigin | Obtain image origin |
| getImageRaster | Obtain image raster-(information) |
| getImageSectionsByBarcode | Obtain image sections by barcode spot |
| getImgAnnArea | Obtain area of image annotation |
| getImgAnnBarcodes | Obtain barcodes by image annotation tag |
| getImgAnnCenter | Obtain center of an image annotation |
| getImgAnnCenterBcsp | Obtain center barcode-spot |
| get_img_ann_helper | Obtain image annotation screening data.frame |
| getImgAnnIds | Obtain unit of method |
| getImgAnnOutlineDf | Obtain image annotation border data.frame |
| getImgAnnRange | Obtain image annotations range |
| getImgAnnSf | Obtain simple feature |
| getImgAnnSummaryDf | Obtain image annotation summary |
| getImgAnnTags | Obtain image annotations tags |
| getInitiationInfo | Obtain information about object initiation |
| getMatrix | Obtain count and expression matrix |
| getModelEvaluationDf | Obtain model evaluation |
| getPixelDf | Obtain pixel data.frame |
| getPixelScaleFactor | Obtain scale factor for pixel to Euol conversion |
| getProjectionDf | Obtain trajectory projection |
| getPrResults | Obtain pattern recognition results |
| getResultsDf | Obtain results stored in data.frames |
| getResultsVec | Obtain screening results stored in vectors |
| getSampleAreaSize | Obtain sample area size |
| getSampleName | Obtain name of 'SPATA2' object |
| getSegmentationNames | Obtain segmentation variable names |
| getSegmentNames | Obtain segment names |
| getSignatureEnrichment | Obtain signature enrichment |
| getSmrdResultsDf | Obtain IAS results (data.frame) |
| getSpataDf | Obtain a spata-data.frame |
| getSpataDir | Obtain SPATA2 object directory |
| getSpatialMethod | Obtain spatial method |
| getSpatialTrajectory | Obtain objects of class 'SpatialTrajectory'. |
| getSpatialTrajectoryIds | Obtain spatial trajectory IDs |
| getSpCorCluster | Obtain cluster results based on spatial correlation analysis |
| getSpCorResults | Obtain spatial correlation results |
| getStsDf | Obtain spatial trajectory screening data.frame |
| getTissueOutlineDf | Obtain outline barcode spots |
| getTrajectoryDf | Obtain a trajectory data.frame |
| getTrajectoryIds | Obtain trajectory ids |
| getTrajectoryLength | Obtain length of trajectory |
| getTrajectoryNames | Deprecated. |
| getTrajectoryScreeningDf | Deprecated |
| getTrajectorySegmentDf | Obtain trjectory course |
| getVariableNames | Obtain variable names |
| ggpInit | Initiate ggplot2 layering |
| ggpLayerAxesClean | Display clean axes |
| ggpLayerAxesSI | Display axes with SI units of length |
| ggpLayerColorGroupScale | Add group specific color spectrum |
| ggpLayer_dummy | ggpLayer |
| ggpLayerEncirclingIAS | Add IAS area expansion |
| ggpLayerFrame | Fix ggplot frame |
| ggpLayerFrameByCoords | Set plot limits |
| ggpLayerGroupOutline | Add group outline |
| ggpLayerHorizonIAS | Add IAS area horizon |
| ggpLayerImage | Add histology image |
| ggpLayerImgAnnOutline | Add borders of annotated structures |
| ggpLayerImgAnnPointer | Add pointer towards image annotations |
| ggpLayerImgAnnRect | Add a rectangular around an image annotation |
| ggpLayerLineplotAid | Add horizontal and vertical lines |
| ggpLayerRect | Add a rectangular to the plot |
| ggpLayerScaleBarSI | Add a scale bar in SI units |
| ggpLayerThemeCoords | Add coordinates theme |
| ggpLayerTissueOutline | Add a hull that outlines the tissue |
| ggpLayerTrajectories | Add trajectory layer |
| ggpLayerZoom | Set plot limits manually |
| ggplot_dummy | ggplot |
| ggplot_family | ggplot_family |
| gradientToModelIAS | Create input for 'model_add' |
| gsdf | The default collection of frequently used gene-sets |
| HistologyImage-class | The 'HistologyImage' - Class |
| HistologyImaging-class | The 'HistologyImaging' - Class |
| hlpr_add_barcode_suffix | Make sure that barcodes are spata-like |
| hlpr_add_old_coords | Adds old coordinates |
| hlpr_adjust_legend_size | Adjusts the size of discrete legend points |
| hlpr_assign_arguments | Assign arguments to calling function |
| hlpr_breaks | Calculates breaks for heatmap according to input matrix |
| hlpr_compare_samples | Compare samples within an object |
| hlpr_dist_mtr_to_df | Convert distance matrix to distance data.frame |
| hlpr_gene_set_name | Removes the class part of a gene set string |
| hlpr_geom_trajectory_fit | Easy switch between geom line and and geom smooth |
| hlpr_image_add_on | Provides the image as ggplot background |
| hlpr_join_with_color_by | Join with single value |
| hlpr_labs_add_on | Return customized ggplot:labs() |
| hlpr_normalize_imap | Normalize gene or gene set values |
| hlpr_normalize_vctr | Normalize gene or gene set values |
| hlpr_one_distinct | Number of distinct values equal to 1? |
| hlpr_process_spatial_correlation_cluster | Process spatial correlation results |
| hlpr_rank_trajectory_trends | Rank trajectory trends. |
| hlpr_save_spata_object | Save spata object inside functions |
| hlpr_scatterplot | Color to + scatterplot helper |
| hlpr_smooth | Smooth variables spatially |
| hlpr_smooth_shiny | Smooth variable spatially in mini-shiny-apps |
| hlpr_subset_across | Subset the across-variables |
| hlpr_summarize_trajectory_df | Join and summarize compiled trajectory data.frames |
| hlpr_vector_projection | Perform vector projection |
| hlpr_widen_trajectory_df | Widen trajectory data.frame |
| identifyTissueOutline | Identify tissue outline |
| identifyTissueSections | Identify tissue sections |
| ImageAnnotation-class | The 'ImageAnnotation' - Class |
| image_annotations | A list of lists of image annotations for specific 'SPATA2'... |
| imageAnnotationScreening | Implementation of the IAS-algorithm |
| ImageAnnotationScreening-class | The 'ImageAnnotationScreening' - Class |
| imageAnnotationToSegmentation | Convert image annotation to segmentation |
| image_dummy | image_dummy |
| include_tissue_outline | Include spatial extent of tissue sections in analysis |
| inferSingleCellGradient | Count cells depending on distance to image annotation |
| initiateSpataObject_10X | Initiate a 'spata2' object from 10X Visium |
| initiateSpataObject_CountMtr | Initiate a 'spata2' object from a raw count matrix |
| initiateSpataObject_Empty | Initiate an empty 'spata2' object |
| initiateSpataObject_Examples | Initiate a 'spata2' object from example data sets |
| initiateSpataObject_ExprMtr | Initiate spata object from scaled expression matrix |
| intersect_polygons | Test polygon intersection |
| is_area | Test area input |
| is_dist | Test distance input |
| 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 |
| legendBottom | ggplot2 legend manipulation |
| loadGeneSetDf | Load gene set data.frame |
| loadGSDF | Original load gene set data.frame |
| loadImageLowres | Load known images |
| loadSpataObject | Load corresponding objects |
| makeContent.resizingSegmentsGrob | Make content for segments grob |
| makeContent.resizingTextGrob | Make content for text grob |
| mapImageAnnotationTags | Image annotation and barcode intersection |
| mergeGroups | Lump groups together |
| mergeTissueSections | Merge tissue sections |
| method_hclust | method_hclust |
| 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 |
| nBarcodes | Number of barcodes |
| nCounts | Number of counts |
| nGenes | Number of genes |
| nImageAnnotations | Number of image annotations |
| normalize | Normalize variable |
| nSpatialTrajectories | Number of spatial trajectories |
| object_dummy | object |
| pb_dummy | pb |
| pheatmap | de_df |
| 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 |
| plotClockplot | Plota clockplot |
| plotCnvHeatmap | Plot CNV Heatmap |
| plotCnvLineplot | Plot CNV Lineplot |
| plotDeaDotPlot | Plot differentially expressed genes |
| plotDeaGeneCount | Plot the number of differently expressed genes of certain... |
| plotDeaHeatmap | Plot differentially expressed genes |
| plotDeaPvalues | Plot the p-value and log fold change distribution of... |
| plotDeaSummary | Plot a summary of differential expression analysis results |
| plotDeaVolcano | Plot gene expression testing results |
| plotDendrogram | dummy |
| plotFourStates | Plot state plot |
| plotGeneDendrogram | Visualize clustering results |
| plotGseaDotPlot | Plot gene set enrichment |
| plotIasBarplot | Plot IAS barplot |
| plotIasEvaluation | Plot IAS evaluation per variable-model pair |
| plotIasHeatmap | Plot IAS heatmap |
| plotIasLineplot | Plot IAS lineplot |
| plotIasLineplotFitted | Plot IAS model fitting |
| plotIasRidgeplot | Plot IAS rideplot |
| plotImage | Plot histology image |
| plotImageAnnotations | Plot image annotations |
| plotImageGgplot | Plot histology image (ggplot2) |
| plotImagesGgplot | Plot histology images (ggplot2) |
| plotMosaicplot | Plot mosaic plot |
| plotOverview | Plot overview of S4 objects |
| plotPcaVariation | Plot Pca Variation |
| plotPseudotime | Monocle3 Pseudotime |
| plotRiverplot | Plot riverplots |
| plotScatterplot | Plot numeric variables as a scatterplot |
| plot_screening_evaluation | Helper |
| plotSpatialTrajectories | Plot spatial trajectory |
| plotStatisticsInteractive | Plot distribution of variables interactively |
| plotSurface | Plot the surface of the sample |
| plotSurfaceAverage | Plot several surface plots colored by gene averages |
| plotSurfaceBase | Plot surface with R base plotting |
| plotSurfaceComparison | Plot several surface plots colored by numeric variables |
| plotSurfaceIAS | Plot screening area of IAS-algorithm |
| plotSurfaceQuantiles | Plot a surface plot colored by binned numeric variables |
| plotSurfaceSC | Plot single cells on surface |
| plotTrajectoryBarplot | Plot categorical trajectory dynamics |
| plotTrajectoryEvaluation | Plot STS evaluation per variable-model pair |
| plotTrajectoryHeatmap | Plot trajectory expression dynamic in heatmap |
| plotTrajectoryLineplot | Plot continuous trajectory dynamics |
| plotTrajectoryLineplotFitted | Plot trajectory model fitting |
| plot_type_dummy | plot_type |
| plotUmap | Plot dimensional reduction |
| plotVolcano | Compare evaluation of spatially opposing fits |
| printAutoencoderSummary | Print autoencoder summary |
| printDeaOverview | Print overview of all conducted de-analysis |
| printDefaultInstructions | Print current default settings |
| print_family | |
| printGeneSetOverview | Print overview about the current gene sets |
| process_expand_input | Process expand input |
| process_ranges | Process input ranges |
| process_seurat_object | Wrapper around Seurat processing functions |
| project_on_trajectory | Project barcode spots on a trajectory |
| project_on_vector | Perform vector projection |
| reduce_vec | Reduces vector length |
| relateToImageAnnotation | Relate observations to an image annotation |
| relevelGroups | Relevel groups of grouping variable |
| removeAnnotation | Remove annotation |
| renameFeatures | Rename features |
| renameGroups | Rename cluster/group names |
| renameImgAnn | Rename image annotation ID |
| resetImageJustification | Reset image justification |
| resizingSegmentsGrob | Used for GeomSegmentFixed |
| resizingTextGrob | Used for GeomTextScaled |
| rotateAll | Rotate image and coordinates |
| rotate_coords_df | Rotate coordinate variables pairs |
| runAutoencoderAssessment | Assessment of Neural Network Set Up |
| runAutoencoderDenoising | Denoise expression matrix |
| runBayesSpaceClustering | Clustering with BayesSpace |
| runCnvAnalysis | Identify large-scale chromosomal copy number variations |
| runDEA | Find differently expressed genes |
| runGSEA | Compute gene set enrichment |
| runPca | Run Principal Component Analysis |
| runSeuratClustering | Clustering with Seurat |
| runSparkx | Identify genes of interest with SPARKX |
| runSpatialCorrelationAnalysis | Initiate gene clustering analysis based on spatial patterns |
| runTsne | Run t-Stochastic Neighbour Embedding |
| runUmap | Run UMAP-Analysis |
| sample_name | sample_name |
| saveGeneSetDf | Save a gene set data.frame |
| saveSpataObject | Save corresponding objects |
| scaleAll | Scale image and coordinates |
| scale_color_add_on | ggplot2 - color add on |
| scale_coords_df | Scale coordinate variable pairs |
| scale_factors | List of scale factors for Visium input. |
| sc_deconvolution | List of data.frames of single cell deconvolution. Names of... |
| section_dummy | Section dummy |
| setActiveExpressionMatrix | Denote the default expression matrix |
| setAutoencoderAssessment | Set results of autoencoder assessment |
| setBarcodes | Set barcodes |
| setCCD | Set center to center distance |
| setCnvResults | Set cnv-results |
| setCoordsDf | Set the coordinates |
| setCountMatrix | Set data matrices |
| setDefault | Set object specific default |
| setDefaultGrouping | Default grouping |
| setDefaultInstructions | Set default instructions |
| setDefaultTrajectory | Obtain dimensional reduction data |
| set_dummy | set |
| setFeatureDf | Set feature data.frame |
| setGeneSetDf | Set the gene-set data.frame |
| setImageAnnotation | Set image annotations |
| setImageDirLowres | Set image directories |
| setImageObject | Set image object |
| setImageOrigin | Set image origin |
| setInitiationInfo | Set initiation information |
| setOutlineVarName | Set outline variable name |
| setPcaDf | Set dimensional reductions data.frames |
| setPixelScaleFactor | Set pixel scale factor |
| setPrResults | Set results of pattern recognition methods |
| setSpataDir | Set SPATA2 directory |
| setSpatialMethod | Set the 'SpatialMethod' object |
| setSpatialMethodInfo | Set information of 'SpatialMethod' object |
| setSpatialMethodSlot | Set slot content of 'SpatialMethod' object |
| setSpCorResults | Set results of spatial correlation analysis |
| setTissueOutline | Set tissue outline |
| setTrajectory | Set trajectories |
| seurat_object_dummy | Title |
| showColors | Show color palettes and spectra |
| showModels | Show spatial gradient screening models |
| smoothSpatially | Smooth numeric variables spatially |
| spata2-class | The 'spata2'- Class |
| SpatialMethod-class | The 'SpatialMethod' - Class |
| SpatialSegmentation-class | The 'SpatialSegmentation' - Class |
| spatial_segmentations | A list of lists of spatial segmentations for specific... |
| SpatialSegment-class | The 'SpatialSegment' - Class |
| spatial_trajectories | A list of lists of spatial spatial_trajectories for specific... |
| spatial_trajectory-class | spatial_trajectory object |
| SpatialTrajectory-class | The 'SpatialTrajectory' - Class |
| spatialTrajectoryScreening | The Spatial Trajectory Screening algorithm |
| SpatialTrajectoryScreening-class | The 'SpatialTrajectoryScreening' - class |
| subsetByBarcodes | Subsetting by barcodes |
| subsetByGenes | Subset by genes |
| summarize_formulas | List of summarizing formulas |
| summarizeIAS | Summarize IAS-results |
| tab_surface_plots_app | Surface plot tab - classic |
| tab_surface_plots_return | Surface plot tab - return |
| theme_lineplot_gradient | ggplot2 themes |
| tissueOutlineIdentified | Check availability of tissue information |
| 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_dist_si_to_pixel | Convert from European Units of Length to pixels |
| 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 |
| transformSeuratToSpata | Transform seurat-object to spata-object |
| transformSpataToCDS | Transform spata-object to cell-data-set (Monocle3) |
| transformSpataToSeurat | Transform spata-object to a seurat-object |
| translate_shape_string | inspired from... |
| update_dummy | update |
| updateSpataObject | Update spata-object from SPATA to SPATA2 |
| validActivationFunctions | Obtain valid argument inputs |
| validation | Validate object input |
| variable | variable |
| variable_num | variable_num |
| variables_num | variables_num |
| Visium-class | The 'Visium' - Class |
| visium_coords | A data.frame that contains all barcode spots of the Visium... |
| vselect | Select vector with tidyselect functions |
