resamplePerplexity {celda} | R Documentation |
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.
resamplePerplexity(counts, celdaList, 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'. |
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. |
celdaList. Returns the provided 'celdaList' with a 'perplexity' property, detailing the perplexity of all K/L combinations that appeared in the celdaList's models.
data(celdaCGSim, celdaCGGridSearchRes) celdaCGGridSearchRes <- resamplePerplexity( celdaCGSim$counts, celdaCGGridSearchRes) plotGridSearchPerplexity(celdaCGGridSearchRes)