resamplePerplexity {celda} | R Documentation

## Calculate and visualize perplexity of all models in a celdaList, with count resampling

### 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, ...)

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

    ## S4 method for signature 'matrix'
    resamplePerplexity(x, celdaList, resample = 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.
`...` | Ignored. Placeholder to prevent check warning.
`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".
`resample` | Integer. The number of times to resample the counts matrix for evaluating perplexity. 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.
`celdaList` | Object of class 'celdaList'. Used only if `x` is a matrix object.

### 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)

[Package celda version 1.6.1 Index]