Heterogeneity measure

A function to measure the heterogeneity of a cell's neighbourhood in terms of entropy. Generally, homogeneous neighbourhoods have low entropy and heterogeneous neighbourhoods have high entropy.

Usage

entropyMeasure(spe, regXclust, threads = 1)

Arguments

spe

SpatialExperiment object with initial cluster and subcluster labels.

regXclust

a list of vectors of each cell's neighbourhood composition indicated by the proportion of initial subclusters it contains.

threads

a numeric value for the number of CPU cores to be used for the analysis. Default value set to 1.

Value

SpatialExperiment object with entropy values associated with each cell.

Examples

data(ClustSignal_example)

# requires list containing cluster proportions of each region (regXclust),
# generated using the neighbourDetect() function
spe <- clustSIGNAL::entropyMeasure(spe, regXclust)
#> [1] "Region heterogeneity calculated. Time 08:51:43"
spe$entropy |> head()
#> [1] 0.46900 0.21084 0.69984 0.35336 0.81185 0.35336