addCoordinates {Spaniel} | R Documentation

## Add coordinates to Object Adds output of Spot Detector coordinates to Seurat object or SCE object created by createSeurat/createSCE. Details about how to use Spot Detector can be found: https://github.com/SpatialTranscriptomicsResearch/st_spot_detector

### Description

Add coordinates to Object Adds output of Spot Detector coordinates to Seurat object or SCE object created by createSeurat/createSCE. Details about how to use Spot Detector can be found: https://github.com/SpatialTranscriptomicsResearch/st_spot_detector

### Usage

    addCoordinates(object, coordinatesFile, scaleFactor = NULL)

### Arguments

`object` | either a Seurat object or SCE
`coordinatesFile` | path to coordinates file exported from Spot Detector
`scaleFactor` | a scaling factor which can be used if the image file has been reduced in size after the coordinates were generated. For example if the image to be used is 10 percent the size of the original factor scaleFactor = 10

### Value

object

### Examples

    ### load a SingleCellExperiment Object
    sceObj <- readRDS(file.path(system.file(package = "Spaniel"),
                            "extdata/sceData.rds"))
    ### path to coordinates file exported from spot detector
    coordinatesFile <-  file.path(system.file(package = "Spaniel"),
                            "spot_positions.tsv")
    sceObj <- addCoordinates(sceObj, coordinatesFile)

[Package Spaniel version 1.8.0 Index]