GetCellGeneDistance {CelliD} | R Documentation |
Small intermediate function for euclidean distance calculation between MCA feature coordinates and cell coordinates. Due to MCA pseudo barycentric relationship, the closer a gene g is to a cell c, the more specific to such a cell it can be considered.
GetCellGeneDistance(X, reduction, dims, features, cells) ## S3 method for class 'Seurat' GetCellGeneDistance(X, reduction = "mca", dims, features = NULL, cells = NULL) ## S3 method for class 'SingleCellExperiment' GetCellGeneDistance(X, reduction = "MCA", dims, features = NULL, cells = NULL)
X |
Seurat or SingleCell Experiment Object |
reduction |
Which dimensionality reduction to use, must be based on MCA. |
dims |
A vector of integers indicating which dimensions to use with reduction embedding and loading for distance calculation. |
features |
Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loading. |
cells |
Character vector of cell names to subset cell coordinates. If not specified will take all cells available from specified reduction Embedding. |
Distance Matrix with genes at row and cells at column