Visualize perplexity of a list of celda models

Source: R/perplexity.R

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

plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 5, alpha = 0.5)

# S4 method for SingleCellExperiment
plotGridSearchPerplexity(x, altExpName = "featureSubset", sep = 5, alpha = 0.5)

# S4 method for celdaList
plotGridSearchPerplexity(x, sep = 5, alpha = 0.5)

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.

altExpName

The name for the altExp slot to use. Default "featureSubset". Only works if x is a SingleCellExperiment object.

sep

Numeric. Breaks in the x axis of the resulting plot.

alpha

Numeric. Passed to geom_jitter. Opacity of the points. Values of alpha range from 0 to 1, with lower values corresponding to more transparent colors.

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)