get_reduced_dimensions_UMAP_bulk {tidybulk} | R Documentation |
Get UMAP
get_reduced_dimensions_UMAP_bulk( .data, .element = NULL, .feature = NULL, .abundance = NULL, .dims = 2, top = 500, of_samples = TRUE, log_transform = TRUE, scale = TRUE, calculate_for_pca_dimensions = 20, ... )
.data |
A tibble |
.element |
A column symbol. The column that is used to calculate distance (i.e., normally samples) |
.feature |
A column symbol. The column that is represents entities to cluster (i.e., normally genes) |
.abundance |
A column symbol with the value the clustering is based on (e.g., 'count') |
.dims |
A integer vector corresponding to principal components of interest (e.g., 1:6) |
top |
An integer. How many top genes to select |
of_samples |
A boolean |
log_transform |
A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data) |
calculate_for_pca_dimensions |
An integer of length one. The number of PCA dimensions to based the UMAP calculatio on. If NULL all variable features are considered |
... |
Further parameters passed to the function uwot |
A tibble with additional columns