CreateCelestaObject: CreateCelestaObject

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

CreateCelestaObject

Description

Initializes the following fields of the Celesta object:

• cell_ID

• original_exp

• marker_exp_matrix

• prior_info

• lineage_info

• total_rounds

• coords

• marker_exp_prob

• nb_list

• cell_nb_in_bandwidth

• cell_nb_dist

• current_cell_type_assignment

• anchor_cell_type_assignment

• starting_cell_type_assignment

• current_scoring_matrix

• current_cell_prob

Usage

CreateCelestaObject(
  project_title,
  prior_marker_info,
  imaging_data_file,
  cofactor = 10,
  transform_type = 1,
  number_of_neighbors = 5,
  bandwidth = 100,
  progress = NULL
)

Arguments

project_title	required name of the project (used in file names)
prior_marker_info	required 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.
imaging_data_file	required segmented imaging data. The first column must contain the cell types to be inferred. The second column must contain the lineage information with the following format (without spaces): # _ # _ #. The first number indicates round. Cell types with the same lineage level are inferred at the same round. An higher number indicates higher cell-type resolution. For example, immune cells -> CD3+ T cells -> CD4+ T cells. The second number indicates the previous lineage cell type number for the current cell type. For example, the second number for CD3+ T cell is 5 because it is a subtype of immune cells which have cell type number 5. The third number is a number assigned to the cell type (i.e. cell type number). The third column and beyond are columns for protein markers. If a protein marker is known to be expressed for that cell type, then it is denoted by a "1". If a protein marker is known to not express for a cell type, then it is denoted by a "0". If the protein marker is irrelevant or uncertain to express for a cell type, then it is denoted by "NA".
cofactor	value used to calculate the arcsinh transform on the protein marker expressions
transform_type	indicates a transform type for the protein marker expressions (0 = no transform, 1 = arcsinh transform)
number_of_neighbors	the number of cells in a single neighborhood
bandwidth	the upper distance bound used when calculating neighborhoods by distance
progress	progress object used for the Shiny app. Do not specify manually.

Value

an initialized Celesta object

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