Man pages for jbergenstrahle/STUtility
Analysis and visualization of Spatial Transcriptomics data
| add.margins | Function used to add whitespace to image |
| AlignImages | Automatic alignment of HE stained tissue images |
| apply.transform | Apply rigid transformation to a set of points |
| ColorBlender | Squeeze 2 or 3 column feature data into the unit cube and... |
| combine.tr | Combines rigid tranformation matrices |
| ConvertGeneNames | Convert gene names |
| CorSpatialDims | Find dims with high spatial autocorrelation |
| CorSpatialGenes | Find genes with high spatial autocorrelation |
| Create3DStack | Creates a stack of point patterns with aligned data and... |
| Create_annotation | Create an annotation |
| create.array.from.feature.vals | Creates an array of dimensions... |
| create.cols.from.array | Creates HSV colors from an array |
| CreateStaffliObject | Create a Staffli object |
| CropImages | Manual cropping of images |
| cscale | Create a plotly compatible colorscale |
| CustomFacetWrap | Custom ggproto object for facet wrap |
| dark_theme | Generates a dark theme for STPlot |
| DimOverlay | Overlay dimensionality reduction vectors on HE images |
| DimPlot3D | Plots a selected dimensionality reduction vector in 3D |
| draw_scalebar | Draws a scalebar for ST plots |
| EdgeMask | Masking function t |
| facet_wrap_custom | Custom facet wrap function |
| FactorGeneLoadingPlot | Plot a bar chart with gene loadings |
| FeatureOverlay | Overlay features on HE images |
| FeaturePlot3D | Plots the values of a selected feature in 3D |
| feature.scaler | Function used to scale numerical features |
| FilterObjects | Get the names of objects within a Seurat object that are of a... |
| find.optimal.transform | Finds optimal transform based on RMSE |
| generate.map.affine | Generate a map function |
| generate.map.rot | Create transformation function |
| GetCoords | Extract table of x, y coordinates from ST count matrix... |
| GetCropWindows | Get crop geometries |
| get.edges | Obtain edges of binary mask stores in masked.masks list |
| get.edges.Seurat | Finds edges of a mask and returns a set of x,y coordinates... |
| get.edges.Staffli | Finds edges of a mask and returns a set of x,y coordinates... |
| getExtension | Obtain file extension |
| GetSpatNet | Create Spatial Networks |
| GetStaffli | Extracts Staffli from Seurat object |
| g_legend | Create legend |
| grid.from.staffli | Creates 2D point patterns for a set of images |
| HSVOverlay | Overlay HSV encoded features on HE images |
| HSVPlot | HSV encoded plots |
| HSVPlot3D | Plots the values of a feature in 3D |
| ica_init | Initiate NMF using ICA |
| icpmat | Match two point sets using iterative closest point search |
| ImagePlot | Function used to plot HE images obtained with 'LoadImages' |
| iminfo | Extracts a list of image info from a Staffli object |
| InputFromTable | Create Seurat object from Spatial Transcriptomics data |
| interpolate_2D_data | Interpolate value across point pattern |
| labelRGB | Select spots by rgb values after ST.DimPlot |
| LoadImages | Function used to read HE images in jpeg or png format |
| make.plot | Used for the manual annotation tool, returns plot and... |
| ManualAlignImages | Manual alignment of images |
| ManualAnnotation | Manual annotation tool via shiny This function takes a seurat... |
| MaskImages | Image masking |
| Merger | Merge expression matrices |
| MergeSTData | Merge two or more Seurat objects containing Staffli image... |
| mirror | Creates a transformation matrix that mirrors an object in 2D... |
| names | Method used to get samplenames from a Staffli object |
| obtain.array.coords | Obtain array coordinates |
| palette.select | Palette selection |
| parse.spot.file | load count files |
| plot | Plot method for Staffli objects |
| prep.sb | Prep scalebar |
| qcGenes | Quality metrics for genes |
| qcSamples | Quality metrics for samples |
| qc.scatter | function(x, y, ...) used to plot the contents of each panel... |
| qcSpots | Quality metrics for spots |
| rasterize_scatter | Assign points to a grid |
| rasterlists | Extracts available image types from Seurat or Staffli objects |
| RegionNeighbours | Autodetect region neighbours |
| rigid.refl | Creates a transformation matrix for reflection |
| rigid.rot | Creates a transformation matrix for rotation |
| rigid.stretch | Creates a transformation matrix for stretching |
| rigid.transf | Creates a transformation matrix for rotation and translation |
| rigid.transl | Creates a transformation matrix for translation with an... |
| rnmf | Run NMF with ica init |
| rotate | Creates a transformation matrix that rotates an object in 2D... |
| RunNMF | Run Non-negative Matrix Factorization |
| samplenames | Extracts available samplenames from Seurat or Staffli objects |
| scaled.imdims | Extracts scaled dimensions of images in Staffli object |
| scale_override | Function used to override scales in facets of a ggplot object |
| scatter_HE | Function used to generate a 2D set of points from an HE image |
| SetQuantile | Find the quantile of a data |
| show | Show method for Staffli objects |
| sleepy | Function to perform system sleep if user having memory issues... |
| slic | SLIC algorithm |
| SmoothPlot | Graphs a smooth interpolation heatmap colored by continuous... |
| spatial_dim_plot | Dimensional reduction plot on ST coordinates on top of HE... |
| spatial_feature_plot | Visualize 'features' on one selected HE image |
| spatial_hsv_plot | Overlay HSVplot on one selected HE image |
| Staffli-class | The Staffli Class |
| Staffli-get-methods | Method used to get meta data from a Staffli object |
| Staffli-set-methods | Method used to set meta data in a Staffli object |
| ST.DimPlot | Dimensional reduction plot on ST coordinates |
| ST.FeaturePlot | Feature plot on ST coordinates |
| ST.ImagePlot | Graphs ST spots colored by continuous variable, e.g.... |
| st.load.matrix | load count files |
| STPlot | Graphs ST spots colored by continuous or categorical features |
| stretch | Stretch along angle |
| ST.rgbDimPlot | Store rgb values after ST.Dimplot OBS! could be merged with... |
| STutility-package | STutility: Analysis and visualization of Spatial... |
| SubsetSTData | Subset a Seurat object containing Staffli image data |
| SummarizeAssocFeatures | Summarize features associated with cselected factors |
| SwitchResolution | Function used to reload images in different quality and apply... |
| translate | Creates a transformation matrix that translates an object in... |
| Warp | Apply warping of x, y coordinates using a affine... |
| WarpImages | Warps images using various transformations |
