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(counts, celdaList, resample = 5, seed = 12345)

### Arguments

`counts` | Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celda.mod'.
`celdaList` | Object of class 'celdaList'.
`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.

### Value

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

### Examples

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

[Package celda version 1.3.4 Index]