R: A class of the output from 'SpaTopic'

gibbs.res-class {SpaTopic}

R Documentation

A class of the output from 'SpaTopic'

Outputs from function SpaTopic_inference. A list contains the following members:

$Perplexity. The perplexity is for the training data. Let N be the total number of cells across all images. Perplexity = exp(-loglikelihood/N)
$Deviance. Deviance = -2loglikelihood.
$loglikelihood. The model log-likelihood.
$loglike.trace. The log-likelihood for every collected posterior sample. NULL if trace = FALSE.
$Beta. Topic content matrix with rows as celltypes and columns as topics
$Theta. Topic prevalent matrix with rows as regions and columns as topics
$Ndk. Number of cells per topic (col) per region (row).
$Nwk. Number of cells per topic (col) per celltype (row).
$Z.trace. Number of times cell being assigned to each topic across all posterior samples. We can further compute the posterior distributions of Z (topic assignment) for individual cells.
$doc.trace. Ndk for every collected posterior sample. NULL if trace = FALSE.
$word.trace. Nwk for every collected posterior sample. NULL if trace = FALSE.