GetCoords: GetCoords

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

GetCoords

Description

Gets the x, y coordinates of each cell

Usage

GetCoords(imaging_data_file)

Arguments

imaging_data_file

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".

Value

the x, y coordinates of each cell

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