Perform spatial deconvolution analysis using RCTD model

Source: R/main.R

Perform spatial deconvolution analysis using RCTD model

RCTD_run(
  sc_data,
  cell_type_columns,
  st_count,
  st_coord,
  output_dir,
  output_name
)

Arguments

sc_data

a Seurat object, denote the single cell RNA reference panel data.

cell_type_columns

a string, the cluster name in the meta data of sc_obj.

st_count

a sparse matrix, denote the count matrix of the spatial transcriptomics data to be deconvoluted.

st_coord

a matrix with two columns, the spatial coordinates.

output_dir

a string, specify the output directory.

output_name

a string, the file name used.

Value

write the results as csv format in the output_dir.