Cluster spacedeconv results

Usage

cluster(
  spe,
  method = c("kmeans", "hclust"),
  data = c("deconvolution", "expression", "pathway", "tf"),
  dist_method = c("correlation", "euclidean", "maximum", "manhattan", "canberra",
    "binary", "minkowski"),
  hclust_method = c("complete", "ward.D", "ward.D2", "single", "average", "mcquitty",
    "median", "centroid"),
  nclusters = 3,
  spmethod = NULL,
  pca_dim = seq(1, 30),
  clusres = 0.5,
  ...
)

Arguments

spe: SpatialExperiment
method: clustering method to be chosen between kmeans and hclust
data: what data to cluster
dist_method: the distance measure to be used if method = hclust
hclust_method: the agglomeration method to be used if method = hclust
nclusters: number of clusters
spmethod: spatial method used fot the clustering, must be dorothea, progeny, expression or the name of the deconvolution method used
pca_dim: PCA dimensions to be used for the clustering of expression data - Seurat::FindNeighbors
clusres: clustering resolution to be used for the clustering of expression data - Seurat::FindClusters