The function CalculateUMAP is used to run UMAP dimensionality reduction.
Usage
CalculateUMAP(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)
# S3 method for iSCMEBObj
CalculateUMAP(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)
# S3 method for iSCMEBResObj
CalculateUMAP(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)
# S3 method for list
CalculateUMAP(obj, reduction = NULL, n_comp = 3, seed = 1, toList = TRUE)Arguments
- obj
A iSCMEBObj object or a iSCMEBResObj object or a list of low dimension embeddings.
- reduction
The name of embeddings to be used to calculate UMAP. If reduction is null, the last added one is used for plotting.
- n_comp
An optional positive integer, specify the number of features to be extracted.
- seed
A random seed to be used.
- toList
An indicator of whether convert the UMAP representation to a list.
Value
Returns a UMAP representation.
Returns a revised iSCMEBObj object.
Returns a revised iSCMEBResObj object.
Returns the UMAP matrix.