calculate_cell_embedding: Calculation of the cell_space parameter needed by CPM

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Calculation of the cell_space parameter needed by CPM

Description

Calculation of the cell_space parameter needed by CPM

Usage

calculate_cell_embedding(
  single_cell_object,
  cell_type_annotations,
  method = c("PCA", "UMAP", "TSNE")
)

Arguments

single_cell_object	A matrix with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set.
cell_type_annotations	A vector of the cell type annotations. Has to be in the same order as the samples in single_cell_object.
method	Either "PCA", "UMAP" or "TSNE"

Value

A matrix with two dimensions. The rows are the cells, the columns are the two dimensions calculated by Seurat

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.