Package index
-
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
-
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
-
FeatureViewer()
- Interactive spatial feature viewer
-
ExportDataForViewer()
- Export data for FeatureViewer
-
ftrviewer()
- Open a feature viewer react application
-
ftrviewerOutput()
renderFtrviewer()
- Shiny bindings for ftrviewer
-
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
-
CoordMirror()
- Mirror coordinates
-
CoordTransform()
- Apply transformations to a set of x, y coordinates
-
get_array_rotation()
- Find array transformation for Visium coordinates
-
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
-
RunNNLS()
- Cell type prediction with NNLS
-
RunMixedNNLS()
- Mixed cell type prediction with NNLS (experimental)
-
CutSpatialNetwork()
- Cut spatial networks in folded tissues
-
AdjustTissueCoordinates()
- Adjust tissue coordinates for digital unrolling
-
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 aSeurat
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
-
mbrain_dataset
- Visium mouse brain dataset
-
mcolon_dataset
- Visium mouse colon dataset
-
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 withSeurat
'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