changeColoringIntensity: Update color intensities for changing to RGB image

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

Update color intensities for changing to RGB image

Description

Update color intensities for changing to RGB image

Usage

changeColoringIntensity(overlay, minInten = NULL, maxInten = NULL, dye)

Arguments

overlay	SpatialOverlay object
minInten	value to change MinIntensity to; NULL indicates no change
maxInten	value to change MaxIntensity to; NULL indicates no change
dye	which dye to change color, can be from Dye or DisplayName column from fluor(overlay)

Value

SpatialOverlay object with updated fluor data

Examples

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

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

fluor(muBrain)

muBrain <- changeColoringIntensity(overlay = muBrain, 
                                   minInten = 500, 
                                   maxInten = 10000, 
                                   dye = "Cy5")

fluor(muBrain)

Nanostring-Biostats/SpatialOmicsOverlay documentation built on Dec. 18, 2024, 9:26 a.m.