spatial_cluster
Short Description
sm.tl.spatial_cluster
: This function allows users to cluster the spatial neighbourhood matrix
genereated by either sm.tl.spatial_expression
, sm.tl.spatial_count
, sm.tl.spatial_lda
etc.
Function
spatial_cluster(adata, df_name='spatial_count', method='kmeans', k=10, n_pcs=None, resolution=1, phenograph_clustering_metric='euclidean', nearest_neighbors=30, random_state=0, label=None, output_dir=None)
Parameters:
Name | Type | Description | Default |
---|---|---|---|
adata |
AnnData object loaded into memory or path to AnnData object. |
required | |
df_name |
string
|
Label of the spatial analysis performed.
By default if |
'spatial_count'
|
method |
string
|
Clustering method to be used- Implemented methods- kmeans, phenograph and leiden. |
'kmeans'
|
k |
int
|
Number of clusters to return when using K-Means clustering. |
10
|
phenotype |
string
|
The column name that contains the cluster/phenotype information. |
required |
n_pcs |
int
|
Number of PC's to be used in leiden clustering. By default it uses all PC's. |
None
|
resolution |
float
|
A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters. |
1
|
phenograph_clustering_metric |
string
|
Distance metric to define nearest neighbors. Note that performance will be slower for correlation and cosine. Available methods- cityblock’, ‘cosine’, ‘euclidean’, ‘manhattan’, braycurtis’, ‘canberra’, ‘chebyshev’, ‘correlation’, ‘dice’, ‘hamming’, ‘jaccard’, ‘kulsinski’, ‘mahalanobis’, ‘minkowski’, ‘rogerstanimoto’, ‘russellrao’, ‘seuclidean’, ‘sokalmichener’, ‘sokalsneath’, ‘sqeuclidean’, ‘yule’ |
'euclidean'
|
nearest_neighbors |
int
|
Number of nearest neighbors to use in first step of graph construction. This parameter is used both in leiden and phenograph clustering. |
30
|
random_state |
int
|
Change the initialization of the optimization. |
0
|
label |
string
|
Key or optional column name for the returned data, stored in |
None
|
output_dir |
string
|
Path to output directory. |
None
|
Returns:
Name | Type | Description |
---|---|---|
adata |
AnnData Object |
1 |
|
Source code in scimap/tools/_spatial_cluster.py
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