Package index • semla

Function reference

Load & process

LoadAndMergeMatrices(): Load and merge multiple gene expression matrices

LoadSpatialCoordinates(): Load and merge multiple coordinate tables

LoadScaleFactors(): Load scale factors

LoadImageInfo(): Load image information

UpdateImageInfo(): Update an image_info tibble

ReadVisiumData(): Read spaceranger output files

LoadImages(): Load images

MergeSTData(): Merge 10x Visium data

SubsetSTData(): Subset 10x Visium data

TileImage(): Tile an H&E image

export_coordinates(): Export spatial coordinates to a JSON file

export_graph(): Export a spatial graph to a JSON file

MapPointsToReference(): Map points to nearest reference spots within a distance

CreateMultiModalObject(): Create a multimodal object in a shared spot coordinate framework

Visualization

MapFeatures(): Map numeric features

MapMultipleFeatures(): Map numeric features or categorical labels

MapLabels(): Map categorical features

MapFeaturesSummary(): Map features spatially and add a summary plot next to it

MapLabelsSummary(): Map features spatially and add a summary plot next to it

ImagePlot(): Plot H&E images

AnglePlot(): Angle plot

centroid_angles_plot(): Draw a centroid angle plot

PlotFeatureLoadings(): Plot feature loadings for dimensional reduction data

scalebar(): Create a scale bar to use for plots

ThemeClean(): Clean theme

ThemeLegendRight(): Move legend to right side

ModifyPatchworkTitles(): Modify patchwork titles

Interactive viewer

FeatureViewer(): Interactive spatial feature viewer

ExportDataForViewer(): Export data for FeatureViewer

ftrviewer(): Open a feature viewer react application

ftrviewerOutput() renderFtrviewer(): Shiny bindings for ftrviewer

Image processing

LoadImages(): Load images

MaskImages(): Mask images

ImageTransform(): Apply rotations and translations to an image

ImageTranslate(): Apply translations

CoordAndImageTransform(): Apply transformation to paired image and coordinates

TileImage(): Tile an H&E image

RigidTransformImages(): Apply rigid transformations to images

RunAlignment(): Manually apply rigid transformations to images

generate_rigid_transform(): Utility function to generate a tibble with image transformations

prep_image(): Prepare images for paper JS react app

Coordinate transformation

CoordMirror(): Mirror coordinates

CoordTransform(): Apply transformations to a set of x, y coordinates

get_array_rotation(): Find array transformation for Visium coordinates

Spatial methods

GetSpatialNetwork(): Create Spatial Networks

DisconnectRegions(): Disconnect regions

RegionNeighbors(): Find region neighbors

CorSpatialFeatures(): Find features with high spatial autocorrelation

RadialDistance(): Calculate radial distances from a region border

RunLocalG(): Calculate local G statistic

RunLabelAssortativityTest(): Label Assortativity Analysis

RunNeighborhoodEnrichmentTest(): Neighborhood Enrichment Analysis

Cell type mapping

RunNNLS(): Cell type prediction with NNLS

RunMixedNNLS(): Mixed cell type prediction with NNLS (experimental)

Digital unroll

CutSpatialNetwork(): Cut spatial networks in folded tissues

AdjustTissueCoordinates(): Adjust tissue coordinates for digital unrolling

Staffli

CreateStaffliObject(): Create a Staffli object

Staffli-class Staffli: The Staffli Class

GetImages(): Method to extract images

GetStaffli(): Method used to extract a Staffli object from the tools slot of a Seurat object

GetImageInfo(): Method to extract image info

GetScaleFactors(): Method to extract image scale factors

GetCoordinates(): Method to extract coordinates

ReplaceImagePaths(): Replace image paths

LoadAnnotationCSV(): Load annotations from a CSV file

show(<Staffli>): Show method for Staffli objects

plot(<Staffli>,<missing>): Plot method for Staffli objects

.DollarNames(<Staffli>) `$`(<Staffli>): Staffli Methods

Data

mbrain_dataset: Visium mouse brain dataset

mcolon_dataset: Visium mouse colon dataset

Misc

UpdateSTUtilityV1Object(): Update an STUtility v1 object to work with semla

UpdateSeuratForSemla(): Update a Seurat object for compatibility with semla

UpdateSeuratFromSemla(): Update a Seurat object created with semla for compatibility with Seurat's spatial functions

file_server(): Host a file server

icp(): Iterative Closest Point algorithm ICP

kabsch(): Kabsch Algorithm

osddu(): Create a react app for digital unrolling

osdduOutput() renderOsddu(): Shiny bindings for osddu

paper(): Create a react app for paper JS in R

paperOutput() renderPaper(): Shiny bindings for paper