Region accessors {lisaClust}

R Documentation

Region accessors for SegmentedCells

Description

Methods to access various components of the 'SegmentedCells' object.

Usage

region(x, imageID = NULL, annot = FALSE)

region(x, imageID = NULL) <- value

Arguments

x	A 'SegmentedCells' object.
imageID	A vector of imageIDs to specifically extract.
annot	Add cell annotation when selecting region information.
value	The relevant information used to replace.

Value

DataFrame or a list of DataFrames

Examples

library(spicyR)
set.seed(51773)

x <- round(c(runif(200),runif(200)+1,runif(200)+2,runif(200)+3,
             runif(200)+3,runif(200)+2,runif(200)+1,runif(200)),4)*100
y <- round(c(runif(200),runif(200)+1,runif(200)+2,runif(200)+3,
             runif(200),runif(200)+1,runif(200)+2,runif(200)+3),4)*100
cellType <- factor(paste('c',rep(rep(c(1:2),rep(200,2)),4),sep = ''))
imageID <- rep(c('s1', 's2'),c(800,800))

cells <- data.frame(x, y, cellType, imageID)

cellExp <- SegmentedCells(cells, cellProfiler = TRUE)


# Generate LISA
lisaCurves <- lisa(cellExp)

# Cluster the LISA curves
kM <- kmeans(lisaCurves,2)
region(cellExp) <- paste('region',kM$cluster,sep = '_')

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