SpatialOverlay-class: Class to Contain NanoString Spatial Overlay Images and Data

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

Class to Contain NanoString Spatial Overlay Images and Data

Description

The SpatialOverlay class organizes the pertinant information from the OME-TIFFs allowing for plotting on top of or beside the image

Usage

  SpatialOverlay(slideName,
                 scanMetadata,
                 overlayData,
                 coords = NULL,
                 plottingFactors = NULL,
                 workflow = list(outline=FALSE,
                                 labWorksheet=TRUE,
                                 scaled=FALSE),
                 image = list(filePath = NULL,
                              imagePointer = NULL,
                              resolution = NULL))

Arguments

slideName	The name of the slide in the SpatialOverlay object
scanMetadata	A list containing the scan metadata: panel(s) used, Physical sizes (x,y) for scale bar, fluorescence data, and segmentation info
overlayData	An SpatialPosition containing individiual sample info: SampleID, Height, Width, X&Y coordinates in overall scan, segmentation, and base64 encoded position
coords	An optional data.frame with coordinates derived from the encoded position.
plottingFactors	An optional data.frame with annotations to plot on. These can be added using addPlottingFactor
workflow	A list containing meta-data on the processing workflow including "outline", "labWorksheet", & "scaled". These booleans are kept automatically in readSpatialOverlay and are used for logic gates in downstream processing
image	A list containing location of and pointer to the image: "filePath", "imagePointer", & "resolution"

Value

An S4 class containing image data from a NanoString GeoMx experiment

Accessing

SpatialOverlay objects have the following accessor methods:

sampNames(object)

extracts the sample names of each ROI in the slide.

slideName(object)

extracts the slide name.

overlay(object)

extracts the SpatialPosition information for each ROI.

scanMeta(object)

extracts the scan metadata.

scanMeta(object)

coords(object): extracts the coordinates for the entire scan.

plotFactors(object)

extracts avaliable plotting factors.

labWork(object)

extracts the boolean if a lab worksheet was used.

outline(object)

extracts the boolena if only the outline points were generated.

seg(object)

extracts if there are any segmented ROIs in the slide.

scaleBarRatio(object)

extracts the scale bar ratio from scanMeta for the X axis

fluor(object)

extracts fluorenscence information for the scan.

showImage(object)

prints image.

res(object)

extracts resolution of image.

workflow(object)

extracts workflow data.

scaled(object)

extracts if coordinates have been scaled.

imageInfo(object)

extracts image data.

See Also

readSpatialOverlay

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