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

Description Usage Arguments Value Examples

Calculates the erplexity of each model's cluster assignments given the provided count matrix, 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.

1	resamplePerplexity(counts, celda.list, resample = 5, seed = 12345)

`counts`	Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celda.mod'.
`celda.list`	Object of class 'celda_list'.
`resample`	Integer. The number of times to resample the counts matrix for evaluating perplexity. Default 5.
`seed`	Parameter to set.seed() for random number generation. Default 12345.

celda_list. Returns the provided ‘celda.list' with a 'perplexity' property, detailing the perplexity of all K/L combinations that appeared in the celda_list’s models.

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celda.CG.grid.search.res = resamplePerplexity(celda.CG.sim$counts, 
                                              celda.CG.grid.search.res)
plotGridSearchPerplexity(celda.CG.grid.search.res)