umap
Short Description
sm.tl.umap
: The function allows users to perform dimensionality reduction using UMAP
Function
umap(adata, use_layer=None, use_raw=False, log=False, n_neighbors=15, n_components=2, metric='euclidean', min_dist=0.1, random_state=0, label='umap', **kwargs)
Parameters:
Name | Type | Description | Default |
---|---|---|---|
adata |
AnnData Object |
required | |
use_layer |
string, optional |
None
|
|
use_raw |
bool, optional |
False
|
|
log |
bool, optional |
False
|
|
n_neighbors |
int, optional |
15
|
|
n_components |
int, optional |
2
|
|
metric |
TYPE, optional |
'euclidean'
|
|
min_dist |
float, optional |
0.1
|
|
random_state |
int, optional |
0
|
|
label |
string, optional |
'umap'
|
|
**kwargs |
Other |
{}
|
Returns:
Name | Type | Description |
---|---|---|
adata |
Modified AnnData object
Embedding stored in |
1 2 3 4 5 |
|
Source code in scimap/tools/_umap.py
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 |
|