Calculate and visualize perplexity of all models in a celdaList

Calculates the perplexity of each model's cluster assignments given the provided countMatrix, as well as resamplings of that count matrix, providing a distribution of perplexities and a better sense of the quality of a given K/L choice.

resamplePerplexity(
  x,
  celdaList,
  useAssay = "counts",
  altExpName = "featureSubset",
  doResampling = FALSE,
  numResample = 5,
  seed = 12345
)

# S4 method for SingleCellExperiment
resamplePerplexity(
  x,
  useAssay = "counts",
  altExpName = "featureSubset",
  doResampling = FALSE,
  numResample = 5,
  seed = 12345
)

# S4 method for ANY
resamplePerplexity(
  x,
  celdaList,
  doResampling = FALSE,
  numResample = 5,
  seed = 12345
)

Arguments

x: A numeric matrix of counts or a SingleCellExperiment returned from celdaGridSearch with the matrix located in the assay slot under useAssay. Rows represent features and columns represent cells. Must contain "celda_grid_search" slot in metadata(x) if x is a SingleCellExperiment object.
celdaList: Object of class 'celdaList'. Used only if x is a matrix object.
useAssay: A string specifying which assay slot to use if x is a SingleCellExperiment object. Default "counts".
altExpName: The name for the altExp slot to use. Default "featureSubset".
doResampling: Boolean. If TRUE, then each cell in the counts matrix will be resampled according to a multinomial distribution to introduce noise before calculating perplexity. Default FALSE.
numResample: Integer. The number of times to resample the counts matrix for evaluating perplexity if doResampling is set to TRUE. Default 5.
seed: Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made.

Value

A SingleCellExperiment object or

celdaList object with a perplexity

property, detailing the perplexity of all K/L combinations that appeared in the celdaList's models.

Examples

data(sceCeldaCGGridSearch)
sce <- resamplePerplexity(sceCeldaCGGridSearch)
plotGridSearchPerplexity(sce)

data(celdaCGSim, celdaCGGridSearchRes)
celdaCGGridSearchRes <- resamplePerplexity(
  celdaCGSim$counts,
  celdaCGGridSearchRes
)
plotGridSearchPerplexity(celdaCGGridSearchRes)