Use other deconvolution methods

create SpaTalk obj and use dec_celltype

Please install the corresponding R/python packages before running

• Use RCTD

obj <- dec_celltype(obj, ..., method = 2)

• Use Seurat

obj <- dec_celltype(obj, ..., method = 3)

• Use SPOTlight

obj <- dec_celltype(obj, ..., method = 4)

• Use deconvSeq

obj <- dec_celltype(obj, ..., method = 5)

• Use stereoscope

# create a stereoscope environment with anaconda3
# define the path of anaconda3, default is "~/anaconda3"
obj <- dec_celltype(obj, ..., method = 6, env = "stereoscope ", anaconda_path = "~/anaconda3")

• Use cell2location

# create a cell2location environment with anaconda3
obj <- dec_celltype(obj, ..., method = 7, env = "cell2location")

• Use the result of other methods directly

❗️❗️❗️ Please check the colnamesand rownames of result first!

# rownames of result
all(rownames(result) == colnames(obj@data$rawdata))
# if not true, then run
rownames(result) <- colnames(obj@data$rawdata)

# colnames of result
all(colnames (result) %in% sc_celltype)
# if not true, then please make them same!

then run

# result must be a matrix
obj <- dec_celltype(obj, ..., dec_result = result)