addCoordinates: Add coordinates to Object Adds output of Spot Detector...

In RachelQueen1/Spaniel: Spatial Transcriptomics Analysis

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)  

RachelQueen1/Spaniel documentation built on May 20, 2021, 5:21 p.m.