plotGridSearchPerplexity {celda} | R Documentation

## Visualize perplexity of a list of celda models

### Description

Visualize perplexity of every model in a celdaList, by unique K/L combinations

### Usage

    plotGridSearchPerplexity(x, ...)

    ## S4 method for signature 'SingleCellExperiment'
    plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 1)

    ## S4 method for signature 'celdaList'
    plotGridSearchPerplexity(x, sep = 1)

### Arguments

`x` | Can be one of A SingleCellExperiment object returned from `celdaGridSearch`, `recursiveSplitModule`, or `recursiveSplitCell`. Must contain a list named `"celda_grid_search"` in `metadata(x)`. celdaList object.
`...` | Ignored. Placeholder to prevent check warning.
`altExpName` | The name for the altExp slot to use. Default "featureSubset".
`sep` | Numeric. Breaks in the x axis of the resulting plot.

### Value

A ggplot plot object showing perplexity as a function of clustering parameters.

### Examples

    data(sceCeldaCGGridSearch)
    sce <- resamplePerplexity(sceCeldaCGGridSearch)
    plotGridSearchPerplexity(sce)
    data(celdaCGSim, celdaCGGridSearchRes)
    ## Run various combinations of parameters with 'celdaGridSearch'
    celdaCGGridSearchRes <- resamplePerplexity(
      celdaCGSim$counts,
      celdaCGGridSearchRes)
    plotGridSearchPerplexity(celdaCGGridSearchRes)

[Package celda version 1.6.1 Index]