Generate scores for cell types for each level
hitype_assign.Rd
Generate scores for cell types for each level
Usage
hitype_assign(
clusters,
scores,
gs = NULL,
fallback = "Unknown",
threshold = 0.05,
top = 10
)
Arguments
- clusters
A named vector of original cluster assignments (names - cell names, values - cluster assignments)
- scores
A list of matrices of cell type scores for each level
- gs
The gene sets prepared by
gs_prepare
Thecell_names
is actually used. One could also passgs$cell_names
directly.- fallback
A fallback cell type if no cell type is assigned
- threshold
A threshold for low confidence cell type assignment The cell types are only assigned for cells with scores higher than the threshold * ncells. (0 - 1, default 0.05)
- top
The number of top cell types to assign for each cluster in the result.
Value
A dataframe with columns: Level
, Cluster
, CellType
and Score
.
For each level and cluster, the top cell types are returned.
You can use summary.hitype_result
to print the combination of
cell types for each cluster.