mapping points between data sets
Usage
point_mapping(
query_signal,
query_assay,
cost,
seed_signal,
seed_assay,
method = "pearson",
neighborhood = "knn",
k = 20,
radius = 0.05,
depth = 1,
batch_size = 10000,
epochs = 1,
use_cost = c("feature", "niche"),
threshold = 0.5,
filter_cells = FALSE,
seed_territory_labels = "Territory",
query_territory_labels = "Territory",
seed_meta_labels = NULL,
query_meta_labels = NULL,
digits = 4,
verbose = TRUE
)Arguments
- query_signal
processed query signal from query assay
- cost
matrix - matrix of size n (query cells) by p (seed cells) containing custom cost matrix.
- seed_signal
processed seed signal from seed assay
- k
int size of niche (knn)
- radius
0.05 proportion of max distance to use as radius for neighborhood
- depth
graph path depth to condsider for neighborhood.
- batch_size
int number of points in each query batch
- use_cost
character string defining how should total cost be computer Available: feature, niche, territory, composition (See details for combinations
- threshold
score threshold below which indicices should be removed. Scores will always be between 0 and 1
- verbose
logical - out progress to console
- query
vesalius_assay object
- seed
vesalius_assay object