dynamo.tl.reduceDimension¶
- dynamo.tl.reduceDimension(adata, X_data=None, genes=None, layer=None, basis='pca', dims=None, n_pca_components=30, n_components=2, n_neighbors=30, reduction_method='umap', embedding_key=None, neighbor_key=None, enforce=False, cores=1, copy=False, **kwargs)[source]¶
Compute a low dimension reduction projection of an annodata object first with PCA, followed by non-linear dimension reduction methods
- Parameters
adata (
AnnData
) – an Annodata objectX_data (
Optional
[ndarray
]) – The user supplied data that will be used for dimension reduction directly.genes (
Optional
[list
]) – The list of genes that will be used to subset the data for dimension reduction and clustering. If None, all genes will be used.layer (
Optional
[str
]) – The layer that will be used to retrieve data for dimension reduction and clustering. If None, .X is used.basis (
Optional
[str
]) – The space that will be used for clustering. Valid names includes, for example, pca, umap, velocity_pca (that is, you can use velocity for clustering), etc.dims (
Optional
[list
]) – The list of dimensions that will be selected for clustering. If None, all dimensions will be used.n_pca_components (
int
) – Number of PCA components.n_components (
int
) – The dimension of the space to embed into.n_neighbors (
int
) – Number of nearest neighbors when constructing adjacency matrix.reduction_method (
str
) – Non-linear dimension reduction method to further reduce dimension based on the top n_pca_components PCA components. Currently, PSL (probablistic structure learning, a new dimension reduction by us), tSNE (fitsne instead of traditional tSNE used) or umap are supported.embedding_key (
Optional
[str
]) – The str in .obsm that will be used as the key to save the reduced embedding space. By default it is None and embedding key is set as layer + reduction_method. If layer is None, it will be “X_neighbors”.neighbor_key (
Optional
[str
]) – The str in .uns that will be used as the key to save the nearest neighbor graph. By default it is None and neighbor_key key is set as layer + “_neighbors”. If layer is None, it will be “X_neighbors”.cores (
int
) – Number of cores. Used only when the tSNE reduction_method is used.
- Returns
adata – An new or updated anndata object, based on copy parameter, that are updated with reduced dimension data for data from different layers.
- Return type