saveConosForScanPy: Save Conos object on disk to read it from ScanPy

Description

Save Conos object on disk to read it from ScanPy

Usage

saveConosForScanPy(
  con,
  output.path,
  hdf5_filename,
  metadata.df = NULL,
  cm.norm = FALSE,
  pseudo.pca = FALSE,
  pca = FALSE,
  n.dims = 100,
  embedding = TRUE,
  alignment.graph = TRUE,
  verbose = FALSE
)

Value

AnnData object for ScanPy, saved to disk

Arguments

con: conos object
output.path: path to a folder, where intermediate files will be saved
hdf5_filename: name of HDF5 written with ScanPy files. Note: the rhdf5 package is required
metadata.df: data.frame with additional metadata with rownames corresponding to cell ids, which should be passed to ScanPy (default=NULL) If NULL, only information about cell ids and origin dataset will be saved.
cm.norm: boolean Whether to include the matrix of normalised counts (default=FALSE).
pseudo.pca: boolean Whether to produce an emulated PCA by embedding the graph to a space with `n.dims` dimensions and save it as a pseudoPCA (default=FALSE).
pca: boolean Whether to include PCA of all the samples (not batch corrected) (default=FALSE).
n.dims: numeric Number of dimensions for calculating PCA and/or pseudoPCA (default=100).
embedding: boolean Whether to include the current conos embedding (default=TRUE).
alignment.graph: boolean Whether to include graph of connectivities and distances (default=TRUE).
verbose: boolean Whether to use verbose mode (default=FALSE)

Description

Usage

Value

Arguments

See Also