GetFinalInferredCellTypes: GetFinalInferredCellTypes

In plevritis-lab/CELESTA: Cell type identification with spatial information

GetFinalInferredCellTypes

Description

Get final cell types and writes two files: the final cell type assignments and the anchor cell type assignments.

Usage

GetFinalInferredCellTypes(
  project_name,
  total_rounds,
  current_cell_type_assignment,
  anchor_cell_type_assignment,
  prior_info,
  lineage_info,
  coords,
  original_exp,
  save_result = T
)

Arguments

total_rounds	the maximum round
current_cell_type_assignment	the current cell type assignments (number_cells x total_rounds)
anchor_cell_type_assignment	the anchor cell type assignments
prior_info	user-defined cell-type signature matrix. The data should contain two columns (name X and Y) for the x, y coordinates and a column for each protein marker. Each row represents the data for a single cell, including its x, y coordinates and expression for each protein marker.
lineage_info	the lineage information from prior_info parsed into round, previous cell type, and cell type number columns
coords	the x, y coordinates of each cell
original_exp	original protein marker expression (containing only the protein markers specified in prior_info)
save_data	whether or not to save the final cell type assignment and anchor cell assignment results

Value

the final cell type assignments

plevritis-lab/CELESTA documentation built on Jan. 30, 2023, 3:32 p.m.