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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

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