readSpatialOverlay: Read in 'SpatialOverlay' from tiff file and annotations

In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

Read in SpatialOverlay from tiff file and annotations

Description

Create an instance of class SpatialOverlay by reading data from OME-TIFF and annotation sheet.

Usage

readSpatialOverlay(
  ometiff,
  annots,
  slideName,
  image = FALSE,
  res = NULL,
  saveFile = FALSE,
  outline = TRUE,
  ...,
  segCol = NULL
)

Arguments

ometiff	path to OME-TIFF
annots	path to annotation file: can be labWorksheet, DA excel file, or delimted file
slideName	name of slide
image	should image be extracted from OME-TIFF
res	resolution of image 1 = largest, higher number = smaller This value will affect the coordinates of the overlays. res = 2, resolution is 1/2 the size as the raw image res = 3, resolution is 1/4 the size as the raw image res = 4, resolution is 1/8 the size as the raw image resolution = 1/2^(res-1)
saveFile	should xml & image be saved, file is saved in working directory with same name as OME-TIFF
outline	returned coordinates only contain outlinearies, will not work for segmented ROIs
...	additional parameters for 'readLabWorksheet' like 'roiCol' and 'slideCol'
segCol	additional parameter for ‘annotMatching' if default search doesn’t work. For default search, set to NULL

Value

SpatialOverlay of slide

See Also

SpatialOverlay-class

Examples

muBrain_GxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip", 
                         package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- readSpatialOverlay(ometiff = image, annots = muBrain_GxT[,1:5], 
                              slideName = "D5761 (3)", image = TRUE, res = 8, 
                              saveFile = FALSE, outline = FALSE)

Nanostring-Biostats/SpatialOmicsOverlay documentation built on April 20, 2024, 5:36 a.m.