Calculate metrics for probability matrix

Calculate metrics for probability matrix

Usage

calcMetrics(spe, pm = NA, pm_cols = NA, val_names = c("entropy", "perplexity"))

Arguments

spe

A SpatialExperiment object.

pm

Optional. The probability matrix.

pm_cols

The colnames of probability matrix. This is requires for SpatialExperiment input. Assuming that the probability is stored in the colData.

val_names

Character vector with length of 2. Column names used to store calculated entropy and perplexity.

Value

A SpatialExperiment object. Calculated entropy and perplexity are saved as columns in the colData of the SpatialExperiment object. Entropy and perplexity are calculated based on information theory:

P(x) is the probability calculated from the scanHoods function.

Entropy H(x) = -P(x)log2(P(x))

Perplexity P(x) = 2^H(x)

By default, the calculated entropy and perplexity will be stored in the colData of the input spe, with column name as entropy and perplexity.

Examples

data("spe_test")

spe <- readHoodData(spe, anno_col = "celltypes")

fnc <- findNearCells(spe, k = 100)

pm <- scanHoods(fnc$distance)
#> Tau is set to: 22747.4

pm2 <- mergeByGroup(pm, fnc$cells)

spe <- mergeHoodSpe(spe, pm2)

spe <- calcMetrics(spe, pm_cols = colnames(pm2))