msmu._tools._umap
umap
umap(mdata, modality, n_comps=2, n_neighbors=None, metric='euclidean', init='random', min_dist=0.1, random_state=0)
Calculate UMAP embedding for a given modality in MuData object.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
mdata
|
MuData
|
MuData object containing the data. |
required |
modality
|
str
|
The modality to perform UMAP on. |
required |
n_comps
|
int
|
Number of UMAP components to compute. Default is 2. |
2
|
n_neighbors
|
int
|
Number of neighbors to use. If None, set to number of samples - 1. Default is None. |
None
|
metric
|
str
|
Metric to use for UMAP. Default is 'euclidean'. |
'euclidean'
|
init
|
str
|
Initialization method for UMAP. Default is 'random'. |
'random'
|
min_dist
|
float
|
Minimum distance parameter for UMAP. Default is 0.1. |
0.1
|
random_state
|
int | None
|
Random state for reproducibility. Default is 0. |
0
|
Returns:
| Name | Type | Description |
|---|---|---|
MuData |
MuData
|
Updated MuData object with UMAP results. |