Preprocessing

The preprocessing module provides basic preprocessing tools. To avoid reinventing the wheel, we won’t repeat methods already in scanpy unless we need functionality not available there.

picturedrocks.preprocessing.pca(data, dim=3, center=True, copy=False)

Runs PCA

Parameters:
  • data (anndata.AnnData) – input data
  • dim (int, optional) – number of PCs to compute
  • center (bool, optional) – determines whether to center data before running PCA
  • copy – determines whether a copy of AnnData object is returned
Returns:

object with obsm["X_pca"], and varm["PCs"] set

Return type:

anndata.AnnData