addPlottingFactor: Add plotting factor to 'SpatialOverlay' object

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

Add plotting factor to SpatialOverlay object

Description

Add plotting factor to SpatialOverlay object

Usage

addPlottingFactor(overlay, annots, plottingFactor, ...)

## S4 method for signature 'NanoStringGeoMxSet'
addPlottingFactor(overlay, annots, plottingFactor, countMatrix = "exprs")

## S4 method for signature 'matrix'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'tbl_df'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'tbl'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'data.frame'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'character'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'numeric'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'factor'
addPlottingFactor(overlay, annots, plottingFactor)

Arguments

overlay	SpatialOverlay object
annots	factor vector with the plottingFactor. if names match sample names in overlay vector will be matched on those, otherwise assumed in the correct order
plottingFactor	name of the new plotting factor
...	if using NanoStringGeoMxSet, name of count matrix to pull counts from
countMatrix	name of count matrix to pull counts from

Value

SpatialOverlay object with new plotting factor

Examples

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

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

muBrain <- addPlottingFactor(overlay = muBrain, 
                             annots = muBrainLW, 
                             plottingFactor = "segment")

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

muBrain <- addPlottingFactor(overlay = muBrain, 
                             annots = muBrainGxT, 
                             plottingFactor = "Calm1",
                             countMatrix = "exprs")

muBrain <- addPlottingFactor(overlay = muBrain,
                             annots = seq_len(length(sampNames(muBrain))),
                             plottingFactor = "ROINum")

head(plotFactors(muBrain))

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

muBrain <- addPlottingFactor(overlay = muBrain,
                             annots = as.factor(seq_len(length(sampNames(muBrain)))),
                             plottingFactor = "ROINum")

head(plotFactors(muBrain))

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