Kandinsky S4 object class

Source: R/00_Kandinsky_Class_funcs.R

Kandinsky is a list object storing spatial data and information for spatial transcriptomic dataset analysed through Seurat.

Slots

platform

sequencing technology

nb

weighted neighbour list object created with the packagespdep

sf

geometry data frame created with the package sf and containing cell/spot coordinates

nb.type

character indicating the neighbouring strategy used to initialize Kandinsky object. Must be one of the following: Q, K, C, M

nnMat

list object containing nearest neighbour matrix created with one of the nnMat functions implemented in Kandinsky

spot_distance

numeric value indicating centroid-to-centroid distance between Visium spots or Visium HD bins

texture

data.frame containing GLCM texture features extracted from Visium H&E slide image

tx

character string indicating the path for the transcript coordinates file from CoxMx/Xenium/Merscope platforms

fov_mask

geometry data frame created with the package sf and containing CosMx FOVs bounding box coordinates

img

Visium H&E or any other tissue slide image stored as a SpatRaster or SpatrasterCollection object via the package terra

mask

masked H&E image obtained via the Kandinsky function he_mask and stored as a SpatRaster or SpatrasterCollection object via the package terra