Perform Hotspot analysis on Vision Object
runHotspot( object, model = "normal", tree = FALSE, number_top_genes = 1000, num_umi = NULL, min_gene_threshold = 20, n_neighbors = NULL, autocorrelation_fdr = 0.05, clustering_fdr = 0.5, logdata = FALSE )
model argument for Hotspot, one of
whether to use tree as latent space. If TRUE, object should have a tree slot.
Hotspot argument for number of genes to consider
optional dataframe containing umi counts in first column for barcodes
minimum number of genes in Hotspot module
number of neighbors to consider in latent space
threshold for significance for genes autocorr
threshold for significance for clustering modules
boolean, log the expression data, avoid for danb Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment and HotspotObject slots of object, as well as recalculates signature scores for new modules.
the modified Vision object