Function used by MapSpatialOmics to align SM data to ST spots with higher resolution (i.e. Xenium cells)
Usage
hiresMapping(
SM.data,
ST.data,
SM.assay = "Spatial",
ST.assay = "Xenium",
SM.fov = "fov",
ST.image = "fov",
SM.pixel.width = NULL,
annotations = TRUE,
add.metadata = TRUE,
map.data = FALSE,
new_SPT.assay = "SPT",
new_SPM.assay = "SPM",
verbose = FALSE
)Arguments
- SM.data
A SpaMTP Seurat object representing the Spatial Metabolomics data.
- ST.data
A Seurat object representing the Xenium Spatial Transcriptomics data.
- SM.assay
Character string defining the Seurat assay that contains the annotated counts and metadata corresponding to the m/z values (default = "Spatial").
- ST.assay
Character string specifying the current assay to use to extract transcriptional data from (default = "Spatial").
- SM.fov
Character string of the image fov associated with the spatial metabolomic data (default = "fov").
- ST.image
Character string matching the image name associated with the ST data stored in the Xenium object (default = "slice1").
- SM.pixel.width
Numeric value defining the width of each SM pixel. If set to
NULL, the median pixel width will be calculated based on the distance between each pixel (default = NULL).- annotations
Boolean value indicating if the Spatial Metabolomics (MALDI) Seurat object contains annotations assigned to m/z values (default = TRUE).
- add.metadata
Boolean defining whether to add the current metadata stored in the SM object to the new mapped multi-omic SpaMTP object (default = TRUE)
- map.data
Boolean indicating whether to map normalised/additional data stored in the
dataslot of the SpaMTP assay. Note: this process is computationally expensive with large datasets (default = FALSE).- new_SPT.assay
Character string defining the assay name of the new overlaid SpaMTP Seurat object containing all updated transcriptomics data (default = "SPT").
- new_SPM.assay
Character string defining the assay name of the new overlaid SpaMTP Seurat object containing all updated metabolomic data (default = "SPM").
- verbose
Boolean value indicating whether to print informative progression update messages and progress bars (default = TRUE).