resamplePerplexity: Calculate and visualize perplexity of all models in a...
In campbio/celda: CEllular Latent Dirichlet Allocation

resamplePerplexity

R Documentation

Calculate and visualize perplexity of all models in a celdaList

Description

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.

Usage

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

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

## S4 method for signature '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)

campbio/celda documentation built on April 5, 2024, 11:47 a.m.