changeImageColoring: Update color scheme for changing to RGB image

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

Update color scheme for changing to RGB image

Description

Update color scheme for changing to RGB image

Usage

changeImageColoring(overlay, color, dye)

Arguments

overlay	SpatialOverlay object, with 4channel image
color	color to change dye to, hex or color name
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")))

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

fluor(muBrain)

muBrain <- changeImageColoring(overlay = muBrain, color = "magenta", 
                               dye = "Cy5")
muBrain <- changeImageColoring(overlay = muBrain, color = "#42f5ef", 
                               dye = "Alexa 488")

fluor(muBrain)

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