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

In conos: Clustering on Network of Samples

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
)

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)

Value

AnnData object for ScanPy, saved to disk

See Also

The rhdf5 package documentation here: <https://www.bioconductor.org/packages/release/bioc/html/rhdf5.html>

conos documentation built on Oct. 17, 2022, 9:07 a.m.