hoodscanR colocalisation — hoodscanR

hoodscanR colocalisation performed by calling the R package hoodscanR through Kandinsky

hoodscanR_coloc(
  data = NULL,
  k = 100,
  label = NULL,
  sample_key = NULL,
  max.cap = 1,
  return.mat = T
)

Arguments

data: Seurat object containing Kandinsky data
k: numeric, number of nearest neighbours to consider for hoodscanR clustering
label: character string specifying the variable name to be used to defne cell annotation groups
sample_key: character string specifying a variable stored in the Seurat object to use as sample/batch annotation. If not NULL, neighbour networks will be defined separately for each sample/batch. Default is NULL
max.cap: numeric, quantile cap to apply to colocalisation coefficients for colour scale creation. Default is 1, will set the coefficient value limit to the highest value of all coefficients
return.mat: boolean, whether returning only colocalization plot (FALSE) or also a dataframe containing colocalization test results

a colocalization plot (when return.mat is FALSE) or a list containing colocalization plot and results in a tabular format

hoodscanR must be installed within the same environmnent of Kandinsky..